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GV Newsletter - November 2020

 


 

GVshared LOVD 2019 

(Usage of the “Global Variome shared LOVD” databases, the primary LOVD installation maintained by Global Variome (https://databases.LOVD.nl/shared), again showed a strong growth in 2019. The number of submitters, people actively sharing data, increased from 2134 (2018) to 2527 (2019). The total number of variants in the GVsharedLOVD increased from 1.05 million to 1.65 million (unique variants from 184,000 to 255,000). The number of individuals/families for which data were shared increased from 988,000 to over 1.2 million. 

Total numbers across all public LOVD installations (# installations, # individuals, # variants) can be found on the LOVD website (http://www.lovd.nl/3.0/public_list). 

Web statistics for the LOVD installations hosted in Leiden (i.e. mainly the “Global Variome shared LOVD”) also showed a steady increase to 500,000 page views per month (2019 total 5.8 million). The number of unique monthly visitors (institutes mostly counted as one visitor) increased to 30,000. While in 2018 79,000 different users visited the LOVD databases, this number doubled to 159,000 in 2019. Annual use of the LOVD api, computer requests for information, increased to over 125 million. 

The GVsharedLOVD databases are a community-owned initiative depending on the support of many volunteers. The databases currently has a Curator for 804 genes (786 in 2018), only a fraction of the 22.992 genes covered. Unfortunately, the request to financially support the databases and send a donation to Global Variome was not followed up by many. 
 

 


The Community Consultation for Proposal SVD-WG009 (conversion), opened in August and was closed in October 2020. The proposal suggests to simplify the recommendations and discontinue the use of variant type "con" to describe conversions. The proposal suggests to use "delins" instead. For details see:

http://varnomen.hgvs.org/bg-material/consultation/svd-wg009/">http://varnomen.hgvs.org/bg-material/consultation/svd-wg009/
 
 


HGVS nomenclature in 2019 

The recommendations for the description of variants in DNA, RNA and protein sequences, HGVS nomenclature, is supported by the Human Genome variation Society (HGVS), Global Variome/Human Variome Project (GV/HVP) and the Human Genome Organisation (HUGO). In 2019 the Sequence Variant Description working group (SVD-WG), the committee authorising the nomenclature, was extended with a new member, Peter Causey-Freeman (Leicester, UK). The SVD-WG completed Community Consultation calls for SVD-WG007 (RNA fusion) and SVD-WG008 (RefSeq) suggesting changes to the nomenclature. Other proposals are in preparation, incl. deletion-insertions, repeated sequences and HGVS/ISCN. End of 2018 HGVS version 19.01 was released (replacing version 15.11). The SVD-WG did not release a new version in 2019. Johan den Dunnen, representing the SVD-WG, participated in the ISCN meeting (Copenhagen, Denmark) preparing the new ISCN2020 version. 

The SVD-WG chair, Johan den Dunnen (Leiden, NL), received ~220 questions about HGVS nomenclature (e-mail and facebook) all of which have been answered. Based on the questions received, 17 facebook posts were made, mirrored on the HGVS twitter. Mostly triggered by questions or remarks received, a range of improvements were made to the HGVS nomenclature website (vArnomen.hgvs.org), correcting errors, adding examples and improving explanation. 

HGVS nomenclature website usage increased from ~400 to ~500 visitors daily (peaking at 650). The 2019 annual total was 154,000 sessions. (121,000 in 2018). 

HGVS nomenclature presentations were given at several national and international meetings / courses / workshops in Nederland, France (Paris), Russia (Moscow), Korea (Seoul) and Denmark (Copenhagen). 

 


We are delighted to announce the Collaboration between the Global Globin Network (GGN) and the International Hemoglobinopathy Research Network (INHERENT). 

For more information, please click here 
 


In 2019 the HGNC was delighted to announce our 40th anniversary. The first full human gene nomenclature guidelines were published in 1979, following discussions at the Human Genome Meeting in Edinburgh, Scotland that year. We are proud to be able to call ourselves one of the longest standing biocuration projects and look forward to taking the project into its fifth decade. 

Additions to our website (www.genenames.org) in 2019 included a new public “curator notes” field to our Symbol Reports, which allows us to add free text to our Reports to clarify certain aspects of the symbol, name or locus type. We further added a new “stable symbol” tag to nearly 2,000 selected symbols on our Report pages, to signify that these are symbols we have manually checked and have no intention of ever changing. This is in response to requests from the clinical community for more stability in gene nomenclature wherever possible. However, some changes are necessary – for example, we also updated the highly problematic set of symbols that were automatically being converted to dates in Microsoft Excel so that this will no longer happen. We also withdrew all approved symbols that had been assigned to the locus type “phenotype only”, as this work has been passed on to our colleagues at OMIM. 

Our sister project, the Vertebrate Gene Nomenclature Committee (VGNC) assigns standardized nomenclature for vertebrate species that lack their own nomenclature committees. In 2019, in addition to naming chimp, dog, cow and horse genes we added macaque and cat to the set of species that we are currently naming. We also updated the VGNC website to enable the release of new gene family data, initially for the complex cytochrome P450 gene family in primates. 

 
 
 

At the next annual meeting of the European Society of Human Genetics (Glasgow, June 12-15 2021), the ESHG will experiment with the organisation of 'pre-meeting courses'. The idea of the pre-meeting courses is to give participants the possibility to get education & training in some general basic genetics-related subjects. The pre-meeting courses will be organised on Friday June 11, under the auspices of the ESHG Education Committee. The first two topics selected are "HGVS nomenclature" (organised by Johan den Dunnen & Raymond Dalgleish) and "ACMG variant classification" (Anna Benet Pages and Andreas Laner).

For further details please follow updates on the ESHG website.
 
 

The BRCA Exchange team at the UC Santa Cruz Genomics Institute is proud to announce the development of a CDH1 Exchange variant portal, through the support of the patient advocacy nonprofit "No Stomach For Cancer". Stomach cancer is the fifth most common type of cancer worldwide, with over 1 million new cases per year globally and 28,000 within the U.S.  Stomach cancer is also deadly, with an average survival five-year survival rate of 29.3%, as it is typically detected in later stages when it has already spread to nearby tissues. Hereditary Diffuse Gastric Cancer (HDGC) is a rare subtype of stomach cancer that arises through genetic risk, and has an earlier age of onset and worse prognosis than most stomach cancers.  Yet these cancers are also preventable. HDGC arises through inherited mutations in a number of genes, most notably CDH1 (Cadherin 1). While individuals who carry harmful CDH1 mutations have an 80% lifetime risk of stomach cancer, and women who carry these mutations also have a 42% lifetime risk of lobular breast cancer, individuals who carry these mutations can manage this risk through screening and risk-reducing surgeries. However, not every mutation to CDH1 affects individuals’ cancer risks. Identifying those mutations that actually increase the risk of cancer is an active area of research, and one in which the UC Santa Cruz Genomics Institute is proud to participate. 
 



Like BRCA Exchange, CDH1 Exchange will share data on CDH1 variants on a web portal that integrates information from public variant repositories including ClinVar, gnomAD and LOVD. The leadership of ClinGen's CDH1 Variant Curation Expert Panel (VCEP) have indicated that LOVD in particular is a rich source of information that they will be excited to see in the CDH1 Exchange portal. LOVD is the data sharing platform of the Global Variome, and the CDH1 gene homepage of LOVD includes data from nations around the globe, including Argentina, Japan, India, Australia and Brazil. Through CDH1 Exchange, this rich information will have greater visibility to scientists, as well as CDH1 variant carriers and their medical providers, to make informed healthcare decisions.

 
 


Upcoming Meetings

Oxford Symposium 'Genomic and Precision Medicine', 11th November 2020 - link to flyer 

Indian Cancer Genetics and Genomics Conference, 20-21 November 2020 - link to flyer 

International Cardiovascular Genomic Medicine Conference, 27-28 November 2020
link to flyer 
 


As many of you know, the original meeting was scheduled to take place in February 2021; however, due to the COVID-19 pandemic, we have decided to postpone the meeting to a date we hope all of you will be able to attend. For more information, please click here
 


We welcome you to the 14th International Congress of Human Genetics (ICHG2022) to be held in Cape, South Africa, proudly hosted by the African Society of Human Genetics (AfSHG) and the Southern African Society for Human Genetics (SASHG).
 
Taking into account the COVID-19 pandemic, we are formally sharing the news that the ICHG will be postponed to 13 – 17 February 2022.
 
Warm regards
Raj Ramesar and Charles Rotimi
(Co-Chairs LOC/ICHG 2021)
 
 
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