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HGNC Newsletter Autumn/Winter 2017

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There are currently 41,276 approved human gene symbols 

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In this newsletter

Thanks to our Scientific Advisory Board

A new beta site for genenames.org is coming soon!

The HGNC-TGMI collaboration

Update on placeholder symbols

New Gene Family Resources

HGNC is tweeting (a bit more than before)

Meeting News

Publication

 


Thanks to our Scientific Advisory Board

We would like to thank the members of our SAB for attending a productive annual meeting, held here at EMBL-EBI from 16-17 November. We were pleased to welcome our new board member, Terence Murphy who heads up the RefSeq group at the NCBI, and we welcomed back our previous board members Todd Taylor, Helen Firth, Fiona McCarthy, Peter Stadler and Eleftheria Zeggini. Thanks especially to Helen who has taken on the duty of chair for 2018 and to Todd for his past years as chair; we are pleased that Todd is willing to remain as a member of the SAB for the coming year.

We also enjoyed meeting face-to-face with our overseas gene family collaborators: Tsviya Olender of the Weizmann Insitute in Israel who works on olfactory receptor (OR) nomenclature, and David Nelson of the University of Tennessee and Jed Goldstone of the Woods Hole Oceanographic Institution in Massachusetts who both work on cytochrome P450 (CYP) nomenclature.

 


A new beta site for genenames.org is coming soon!

We are in the process of creating a new beta site for genenames.org. We will be asking for feedback once this goes live in the new year so please watch this space!

 


The HGNC-TGMI collaboration

The Transforming Genetic Medicine Initiative (TGMI) is creating a curated list of genes causally associated with Mendelian genetic disease, called the Gene Disease Map. Our main contribution to this effort are HGNC-approved gene symbols and gene names, together with stable, unique identifiers, HGNC IDs. The gene symbols can be used in reporting genetic variants and the HGNC IDs are ideal for linking biomedical data resources, such as OMIM, Ensembl and NCBI RefSeq. Our aim is always to minimise changes to gene symbols, but as part of the TGMI effort we have been formulating criteria for stabilising gene nomenclature.

 


Update on placeholder symbols

We are working hard to update the nomenclature of placeholder symbols, including the C#orf$ and KIAA symbols. In C#orf$s, the # represents the chromosome on which the gene is located, and $ is the next number in a numerical series. The KIAA symbols originate from the Kazusa ORFeome Project, where newly identified human genes were assigned the 'KIAA' root with a unique four digit number. KIAA symbols were approved for genes where no other information was available, but were used instead of a C#orf$. We are aiming to replace both C#orf$ and KIAA symbols once information on the structure, function or homology of the gene becomes available. This ties in with two of the major aims of our project: the stabilisation of gene symbols mentioned above and the transferral of human nomenclature across species as part of the VGNC project.

Some examples of renames from the last few months are....

C9orf172 - new symbol: AJM1, name: apical junction component 1 homolog

C10orf10 - new symbol: DEPP1, name: DEPP1, autophagy regulator

C11orf63 - new symbol: JHY, name: junctional cadherin complex regulator

C1orf27 - new symbol: ODR4, name: odr-4 GPCR localization factor homolog

C1orf186 - new symbol: RHEX, name: regulator of hemoglobinization and erythroid cell expansion

KIAA0907 - new symbol: KHDC4, name: KH domain containing 4, pre-mRNA splicing factor

KIAA1683 - new symbol: IQCN, name: IQ motif containing N

KIAA1644 - new symbol: SHISAL1, name: shisa like 1

Please let us know if you have information on any C#orf$ or KIAA genes that would help us with this renaming effort by contacting us at hgnc@genenames.org or using our gene symbol request form.

 


New Gene Family Resources

Notable new gene family pages include:

Our first two families representing networks: the Constitutive centromere associated network and the KMN network, which is subdivided into the KNL1 complex, the MIS12 kinetochore complex and the NDC80 kinetochore complex.

We have also created gene families for a few more complexes, including the multienzyme Purinosome, the highly conserved CTLH complex and the endosomal cargo recycling Retriever complex.

Please contact us if you work on a gene family that is missing from our resource, or if you have further information about any of our exisiting gene families.

 


HGNC is tweeting (a bit more than before)

We would like to remind everyone that we have a Twitter account, @genenames. Over the last few months we have been trying to raise our social media profile by tweeting more regularly. Please follow us to see what we have to say!

 


Meeting News

Beth attended the Animal Genetics and Diseases  meeting here on campus at Hinxton, UK from 20-22 September where she presented a poster and gave a lightning talk on our VGNC work. Elspeth, Bryony and Ruth had campus enrolments to this meeting so were able to attend some of the talks and coffee breaks to meet with delegates.

Elspeth met all of ourNC-IUPHAR collaborators at their meeting in Paris, France from 13-15 October, while Paul travelled to Orlando, USA for ASHG2017
from 17-21 Octoberwhere he presented a poster explaining how and why HGNC IDs should be used.

Elspeth and Ruth attended the RNAcentral Consortium Meeting on campus in Hinxton, UK from 6-7 November 2017. They enjoyed meeting several of our RNA specialist advisors and collaborators and taking part in workshops about the RNAcentral resource. We were all happy to hear that genenames.org is now the second top referrer of traffic to RNAcentral following the addition of links from our Symbol Reports to their resource this year.

In January Beth and Susan will be attending International Plant & Animal Genome (PAG) XXVI in San Diego, USA where they will be taking part in the EBI workshop and presenting a poster on our VGNC work.

 


Publication

Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD.Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.Nucleic Acids Res. Epub 2016 Oct 30. PMID: 29126148 DOI:10.1093/nar/gkx1031

 


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