Welcome to Paul
We are pleased to announce that we have a new member of the curation team. Dr Paul Denny joined us at the start of December following his position as a Gene Ontology curator at University College London (UCL), where he specialised on the curation of human genes relevant to Parkinson’s. Paul has a BSc in Biomolecular Science from the University of Portsmouth and a PhD in the Molecular Biology of the brain from the Royal Postgraduate Medical School at Hammersmith hospital.
Introducing the VGNC!
We are excited to announce the public launch of our VGNC (Vertebrate Gene Nomenclature Committee) project. The aim of the VGNC is to assign standardised gene symbols and names for vertebrate species that currently lack a nomenclature committee. Where there is a one-to-one ortholog with human the gene symbols in both species should be exactly equivalent. The most challenging aspect will be assigning nomenclature within complex gene families where there will often be many-to-many homology relationships across species. For these families we aim to work with experts in the field; our current funding has enabled us to collaborate with Drs Jed Goldstone and David Nelson on naming within the vertebrate cytochrome P450 family, and with Drs Doron Lancet and Tsviya Olender on naming olfactory receptors across vertebrates.
We have used chimp as a prototype to begin our naming across species, due to the similarity between the chimp and human genomes coupled with the quality of the chimp genome assembly. You can read more on the methods we have used to transfer symbols from human to chimp orthologs in the ‘ Naming chimp genes’ section of our previous newsletter. We have now named over 14,500 chimp genes and released our dedicated VGNC website, vertebrate.genenames.org, where you can view and download this data. The vertebrate.genenames.org website has a consistent look and feel with www.genenames.org, except that it uses a beautiful green colour in order to be easily distinguished; in addition it can be accessed via a VGNC portal in the toolbar of www.genenames.org. You can browse all of our chimp symbols via the ‘Gene data’ tab on vertebrate.genenames.org and there is a prominent search tool that can be used to find individual genes or groups of genes. We also provide options to download either the full chimp dataset or data for each chimp chromosome via the ‘Downloads’ tab on vertebrate.genenames.org. Each chimp gene with approved nomenclature has its own Symbol Report; please see the CDH9 report for an example. Where available, there is a link back to the Symbol Report for the human ortholog on www.genenames.org. We also provide links to the relevant chimp gene pages in Ensembl and NCBI Gene; these two projects are currently using VGNC chimp gene symbols, so we have already provided standardised naming for around 75% of the protein coding genes in this species.
We are continuing to name chimp protein-coding genes and providing daily data releases on vertebrate.genenames.org. Future plans include extending our naming effort to genes in dog and cow.
CCDS survey
The NCBI, on behalf of the CCDS collaboration (of which HGNC are a member), are currently running a survey that will help assess how the human and mouse Consensus CDS (CCDS) data is being accessed and used by the scientific community. Data gathered from the survey will help to plan the future direction of the CCDS project. The survey is available on the CCDS webpage ( https://www.ncbi.nlm.nih.gov/projects/CCDS/). If you use CCDS data, please take time to leave your feedback and suggestions on this project.
New Gene Family pages
Our gene families resource continues to grow and we are proud to report that we now have over 1000 gene family pages! New gene families include BRCA1 A complex, BRCA1 B complex, BRCA1 C complex, BTG/Tob family, doublecortin superfamily, I-BAR domain containing, NineTeen complex, Scribble complex, Shelterin complex, SIBLING family and STRIPAK complex.
Please let us know if you are working on a gene family that is missing from our resource.
Gene Symbols in the News
We are sharing some food and drink-related news stories featuring approved gene symbols ahead of the festive season. First, a study has reported a link between carriers of a particular MC4R gene variant and a liking of fatty over sugary foods; carriers of the variant opted for high rather than low fat chicken korma but showed a lower preference for high rather than low sugar Eton Mess. Food-loving Labradors with weight problems have been shown to carry a variant of the POMC gene and the POMC gene has also been linked to obesity in humans. A study in Edinburgh has linked reduced coffee consumption with a variant of the PDSS2 gene with the researchers suggesting that the cells of these individuals have a lower ability to breakdown caffeine.
Meeting News
In September 2016 Beth, Susan and Elspeth attended the Livestock Genomics Meeting 2016 in Cambridge where Susan gave a presentation on our VGNC work, then Kris and Elspeth attended Genome Informatics 2016 at the Hinxton Genome Campus where they presented two posters, one on our gene families and the other was on the VGNC.
October saw Kris attending talks at OSCON (Open Source Convention) 2016 in London, Susan presenting a poster on the VGNC at ASHG2016 in Vancouver, Canada and Elspeth enjoying the Autumn NC-IUPHAR Meeting in Paris, France where she talked about recent developments within the HGNC.
Publications
de Castro F, Seal R, Maggi R. ANOS1: a unified nomenclature for Kallmann syndrome 1 gene (KAL1) and anosmin-1. Brief Funct Genomics 2016 Nov 29. pii: elw037. [Epub ahead of print] PMID: 27899353
Yates B, Braschi B, Gray K, Seal R, Tweedie S, Bruford E. Genenames.org: the HGNC and VGNC resources in 2017. Nucleic Acids Res. 2016 (Database Issue) [Epub ahead of print] PMID: 27799471 doi: 10.1093/nar/gkw1033
Gladyshev VN, Arnér ES, Berry MJ, Brigelius-Flohé R, Bruford EA, Burk RF, Carlson BA, Castellano S, Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohé L, Green FR, Guigó R, Handy DE, Hatfield DL, Hesketh J, Hoffmann PR, Holmgren A, Hondal RJ, Howard MT, Huang K, Kim HY, Kim IY, Köhrle J, Krol A, Kryukov GV, Lee BJ, Lee BC, Lei XG, Liu Q, Lescure A, Lobanov AV, Loscalzo J, Maiorino M, Mariotti M, Prabhu KS, Rayman MP, Rozovsky S, Salinas G, Schmidt EE, Schomburg L, Schweizer U, Simonović M, Sunde RA, Tsuji PA, Tweedie S, Ursini F, Whanger PD, Zhang Y. Selenoprotein Gene Nomenclature. J Biol Chem. 2016 Nov 11;291(46):24036-24040. PMID: 27645994
Marenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C. ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. Database (Oxford) 2016 Oct 2. PMID: 27694208 PMCID: PMC5045865
Nebert DW, Dong H, Bruford EA, Thompson DC, Joenje H, Vasiliou V. Letter to the editor for “Update of the human and mouse Fanconi anemia genes”. Hum Genomics 2016 2016 Jul 4;10(1):25. PMID: 27377885 PMCID: PMC4932714