Solving the :: Fusion Nomenclature Challenge for File and Directory Naming

Tom Bisson; Stefan Kaluziak; Norman Zerbe; Jochen K Lennerz

doi:10.1016/j.jmoldx.2025.08.002

Solving the :: Fusion Nomenclature Challenge for File and Directory Naming

J Mol Diagn. 2025 Sep 1:S1525-1578(25)00198-9. doi: 10.1016/j.jmoldx.2025.08.002. Online ahead of print.

Authors

Tom Bisson¹, Stefan Kaluziak², Norman Zerbe³, Jochen K Lennerz⁴

Affiliations

¹ Institute of Medical Informatics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany; Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany. Electronic address: tom.bisson@charite.de.
² Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
³ Institute of Medical Informatics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany; Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany; Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany.
⁴ BostonGene, Waltham, Massachusetts.

PMID: 40902725
DOI: 10.1016/j.jmoldx.2025.08.002

Abstract

Following recommendations from various consortia and professional societies, the double colon symbol (::) has become an integral part of gene fusion nomenclature (eg, EML4::ALK). Although widely adopted, its use presents technical challenges, as many common operating systems restrict the use of colons (:) in file and directory names. Consequently, the double colon (::) is often replaced with an underscore (_) or other allowed characters, introducing ambiguity and inconsistency. The first objective of this work is to raise awareness of this issue. The second objective is to propose a simple technical solution, that is, replacing the command-carrying symbol with a visually similar and functionally distinct ASCII character. The technical solution includes confirmation of functional compatibility and visual compliance with the established fusion nomenclature. The proposal also includes using Unicode characters to replace the slash (/) for alternative variants, the greater than symbol (>) for substitutions, and the asterisk (∗) for nonsense variants, for example. To support consistency, keyboard shortcuts or custom scripts may be used to automate these substitutions. The straightforward solution presented in this paper counterbalances unintended technical consequences and thereby promotes harmonization towards a unified genomic variant nomenclature.