100% of journal submissions contain gene/variant nomenclature errors
A systematic two-year review of manuscripts submitted to Genetics in Medicine found that every single submission contained noncompliant gene or variant nomenclature, with errors expected to significantly reduce variant findability in database searches. Testing across three open-source tools confirmed that erroneous nomenclature hampers variant discovery. The authors propose strategies for implementing nomenclature-focused technical editing within journal editorial workflows.
The original study
Universal Presence of Gene/Variant Nomenclature Errors in Journal Manuscript Submissions.
- Authors
- Lansdon LA, Porath B, Mori M, Miller DT, Dunham Drexler D, Wattenberg C, et al.
- Journal
- Clinical chemistry
- PMID
- 41793390
Original abstract
BACKGROUND: Accurate descriptions of human genomic variants are crucial for gene-disease association, discovery, and clinical diagnosis. Although standardized genomic nomenclature, expertly curated and promulgated by the Human Genome Variation Society and the International Standing Committee on Human Cytogenomic Nomenclature, is strongly encouraged in scientific publications, many journals lack systematic mechanisms to ensure compliance with these nomenclature standards. METHODS: Genetics in Medicine developed detailed author instructions for gene/variant nomenclature and a protocol for scientific editorial teams, which promote adherence to gene/variant nomenclature standards in published works. We present results from a systematic review of manuscripts submitted over a 2-year period, applying a standardized rubric and severity scoring system based on this protocol. In addition, we assessed how erroneous variant nomenclature published in 4 different manuscripts affects findability using 3 open-source tools. RESULTS: Of submitted manuscripts, 100% demonstrated noncompliance with current nomenclature standards. Furthermore, every manuscript contained one or more errors expected to significantly reduce the probability of variant findability during routine database searches and/or variant curation efforts. Findability was complicated by differences inherent to each database or search engine's structure, resulting in an additional layer of variability in the literature returns. CONCLUSIONS: We conclude that strict adherence to gene/variant nomenclature standards is critical in published works, and that rigorous author instructions are insufficient to ensure adherence to nomenclature standards. In addition, we share strategies for the implementation of technical, nomenclature-focused editing within a journal's editorial framework to promote improved genomic variant findability.