The Nomenclature of Human and Vertebrate Genes

University Of Cambridge, Cambridge

Investigators

Linked publications, trials & patents

Abstract

PROJECT SUMMARY (HG003345) Naming systems are crucial in all walks of life, especially in science and clinical medicine where accuracy and reproducibility are vital. The HUGO Gene Nomenclature Committee (HGNC) is the only group worldwide that has provided standardized naming for human genes. HGNC’s symbols, names and identification numbers (IDs) enable effective communication and exchange of information between anyone interested in genes. The first aim of this application carries on this crucial work, focussing on naming newly identified protein coding loci, both within the current reference genome and in new pangenome haplotypes, and continuing systematic naming of pseudogenes and RNA genes. Utilizing data arising from a variety of methods including deep learning we will continue to update nomenclature for newly characterised loci, genes with uninformative placeholder symbols, and in rare cases where existing nomenclature is proven to be misleading. This aim also recognises the need for stability in nomenclature, especially for genes associated with phenotypes. HGNC will review protein coding genes with informative names and aim to stabilize symbols for the majority of well characterized genes. Aim 2 will expand into the field of transcript naming; to date this has been restricted to a very small set of complex loci (e.g. protocadherins). In collaboration with the biocuration groups from NCBI and EMBL-EBI, HGNC will work with the community to establish guidelines for transcript naming, and provide standardized names (and stable HGNC IDs) for well-defined transcripts. Aim 3 will pursue HGNC’s role in coordinating gene naming across vertebrates, through collaboration with the existing nomenclature committees for mouse, rat, chicken, Xenopus and zebrafish, and through work as the Vertebrate Gene Nomenclature Committee (VGNC). Established by the HGNC in 2016, to date the VGNC has named over 112,000 genes across key species (chimpanzee, macaque, cattle, pig, horse, dog, cat), using a combination of automation and manual curation. These efforts will be broadened to include naming in Chiroptera from the Bat 1K project, both to expand VGNC’s taxonomic range and due to their intriguing antiviral immune responses. Building on the HGNC and VGNC’s existing gene group resources, and in collaboration with experts, gene nomenclature will be standardized across vertebrates in complex families including the C2H2 zinc fingers, immunity related genes such as the MHC locus, and pharmacogenetically relevant genes. This aim will include development of a pipeline for phylogenetic and syntenic analysis in complex families. In Aim 4 HGNC will engage with stakeholders to encourage compliance with approved gene nomenclature, working with journal editors and publishers. Awareness of HGNC’s resources, especially within the clinical community, will be raised via direct engagement, and through channels such as Twitter/X and the genenames.org blog, while the number of video tutorials will be expanded. The use of approved nomenclature is vital to avoid confusion and wasted experiments in the laboratory, and to reduce the potential for patient harm.