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HGNC Newsletter Autumn 2008

< Nome News Issues There are now over 26000 approved symbols

The launch of our HGNC Newsletter

This newsletter marks the beginning of our newly-titled 'HGNC Newsletter' in place of the previous newsletter, Nome News. The new name reflects the many changes that have occurred recently in the project, such as the new website address (www.genenames.org), the new e-mail address (hgnc@genenames.org) and the relocation of the project to the EBI in Hinxton.

Two new staff members

We'd like to introduce our two new gene nomenclature advisors, Susan Gordon and Ruth Seal, who both joined the project in May. Susan conducted research on the molecular basis of Fanconi anaemia during her Ph.D. studies at the Hospital for Sick Children Research Institute (University of Toronto). This was followed by a postdoctoral fellowship in molecular phylogenetics at the Great Lakes Institute, Windsor, Canada, after which she joined the HGNC. Ruth completed a Ph.D. on mRNA stability in human cells at the University of Newcastle upon Tyne and then worked as a literature curator at FlyBase before joining the HGNC.

A new feature: locus types

We have added a new data class to the 'Core Data' section of our symbol reports: locus types. These data are manually curated and provide information on the genetic class of each approved symbol. Examples of locus types are 'gene with protein product', 'RNA, small nucleolar' and 'pseudogene'.

New links to external databases

We have added CCDS IDs, where relevant, to our gene reports. The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. As we do not curate all variants of a gene, only one CCDS per gene is displayed. We have also added links to the wikigenes project, a resource that allows researchers to edit gene pages with their own information. Additionally, we have added two extra data sources to our specialist database links: COSMIC and Orphanet. Genes that have been found to be mutated in tumors will have a link to the relevant gene page of COSMIC, while genes that have been implicated in the pathology of rare diseases will have a link to Orphanet.

HCOP Update

The HGNC Comparison of Orthology Predictions search tool, HCOP, has been updated with the addition of UCSC as an extra source of orthology assertions between human and the species mouse, rat and zebrafish. We plan to add orthology data for the species cow, C. elegans and S. cerevisiae to HCOP in the near future.

Coming soon: BioMart for HGNC

We are in the process of developing an HGNC BioMart query tool to allow efficient complex mining of our data. Other sites that have BioMart tools include Ensembl, WormBase and Reactome.Visit http://www.biomart.org/ for more information on BioMart software.

ncRNA genes

Matt recently attended the 13th annual meeting of the RNA Society held in Berlin, Germany from 28th July to 3rd August. He presented a poster detailing the progress we've made in naming all of the small classical non-coding RNA (ncRNA) genes, such as the ~500 transfer RNA genes that we recently named in co-ordination with the Genomic tRNA Database. He also canvassed researchers on potential naming schemes for the large ncRNA genes and, as a result, we have now agreed the stem symbol NCRNA# (non-protein coding RNA #) for all human large (>300nt) ncRNAs with a processed transcript and/or strong EST evidence. NCRNA# symbols are temporary placeholders until there is functional information on which to name an ncRNA gene.  

Other Meetings Attended in 2008

Genomic Disorders (Hinxton, UK) 17-20 March
NC-IUPHAR Meeting (Paris, France) 18-20 April
The Biology of Genomes (Cold Spring Harbor, USA) 6-10 May
HGVS Meeting
(Barcelona, Spain) 31 May
European Human Genetics Conference ESHG
(Barcelona, Spain) 31 May-3 June
International Congress of Genetics (Berlin, Germany) 19-23 July
The eighth CSHL/Wellcome Trust conference on Genome Informatics (Cambridge, UK) 10-14 September

Forthcoming meetings

Elspeth will be attending the HGM2008 meeting in Hyderabad, where we are sharing booth 57 with Ensembl. Matt & Elspeth will both be at this year's ASHG conference in Philadelphia, where we will be sharing booth 1203 with the Human Genome Organisation. Please visit us at either meeting if you have any queries about the work of the HGNC.

Publications

Kampinga HH,...Bruford EA, et al. Guidelines for the nomenclature of the human heat shock proteins. Cell Stress Chaperones. 2008 Jul 29. PMID: 18663603

Heisterkamp N, Groffen J, Warburton D, Sneddon TP. The human gamma-glutamyltransferase gene family. Hum Genet. 2008 Mar 21. PMID: 18357469

Ting JP, Lovering RC, et al. The NLR gene family: a standard nomenclature. Immunity. 2008 Mar;28(3):285-7 PMID: 18341998


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