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GV Newsletter - October 2021



More information, please visit: https://www.hugo-hgm2022.org/
 
 

We are proud to announce that Professor Johan den Dunnen has been bestowed upon the royal title of "Officer of the Order of Orange-Nassau" by the King of the Netherlands, represented by the mayor of Leiden, Mr. H. Lenferink. Johan received this royal recognition for: his dedication to make the latest genomic technologies available to researchers through the Leiden Genome Technology Center (LGTC), his research in particular on muscular dystrophies and the development of the exon skipping therapy, his efforts to get to an international standard for the description of genetic variants (the HGVS nomenclature), his commitment to the public sharing of genetic variant data through establishing the Leiden Open Variation Database (LOVD) platform, his enthusiasm to share his knowledge on DNA and genomic technologies with students of any background, and his role in the initiation of "LeveDNA!", a Dutch foundation to explain everything about DNA to the layman. These contributions to science and society were highlighted in an entertaining speech by the mayor, after which he pinned on the medal.
 
Johan den Dunnen officially retired in July of this year and celebrated his retirement and his achievements of the last few decades with a small group of family and close colleagues last Thursday, September 30.

 
 


HGVS nomenclature Q&A sessions have started!
 
The sessions start with a brief welcome from Johan den Dunnen, chair of the HGVS nomenclature committee. Next, a series of prepared questions for the participants to answer using the DirectPoll system. Participants are able to see each other’s answers anonymously. After each question, the answers are revealed and explained.  We want to hold these sessions, giving people a chance to practice and discuss in a safe environment. After the prepared questions, there is time for participants to ask specific questions directly.
 
For those interested to give it a try, the Q&A session is available aftwewards using Socrative, classroom HGVSonline (https://api.socrative.com/rc/ibPQGW).
 
 
Our next session will take place on Tuesday 26th October at 8am UTC. We have alternated the timings of each session to accommodate all time zones. For your time zone, please click here
 
To register for the next session, please click here. You can also see this event listed on the Human Genome Organisation’s(HUGO) Facebook page. We record the meeting for those not able to join. 
 
 
The questions from the Q&A session will be taken from those we receive daily and be a mix of simple and more complex cases. The idea is that you train yourself and learn HGVS nomenclature by applying the recommendations. For those not able to participate, the questions will be available afterwards using the Socrative platform (www.Socrative.com, classroom to be announced).  For the 'questions from participants' session, everybody is encouraged to send questions to VarNomen@HGVS.org so we can prepare. Of course, we will also allow you to ask questions 'live'.
 
 
If you have any comments, suggestions or questions you would like answered for these sessions, please let us know. 
 
Interested to support the HGVS nomenclature work? Please consider sponsoring one of the bi-monthly meetings. For details, please contact amy@variome.org">amy@variome.org. Of course, we will acknowledge sponsorship in advertisement and during the meeting.
 
 

HGVS nomenclature

On Friday October 8, the Sequence Variant Description working group (SVD-WG) had its first online meeting. On the table were subjects like; the collaboration between HGVS, HVP/GV and HUGO, membership of the SVD-WG of the new HUGO Nomenclature Standards committee, the Terms of reference of the SVD-WG, membership of the working group and the election of new members. In addition, the SVD-WG discussed the comments that were received for Community Consultation proposal SVD-WG010 (http://varnomen.hgvs.org/bg-material/consultation/svd-wg010/">http://varnomen.hgvs.org/bg-material/consultation/svd-wg010/), the var-distance proposal. The working group decided that more time was needed to discuss the comments received and a final decision remains pending.
 
 

NEW members for HGVS nomenclature committee

The HGVS nomenclature committee, the Sequence Variant Description working group (SVD-WG), is looking for new members. In a next newsletter we will give details on when and how to apply.
 

Do you want to get involved? 
Please prepare to apply!

 

Variant Effect Prediction Training Course

21 - 23 September 2021

Online

The 5th Variant Effect Prediction Training Course was held from the 21st -23rd September. Originally scheduled to take place in Barcelona in 2020 it was postponed due to COVID-19 and was transformed from an in-person to a virtual course this year.  Three days of live streaming, connected 280 attendees from 40 countries and 105 cities for 3 days packed with expert speakers and interesting sessions.

The three-day program covered many themes related to variant interpretation starting with the “basics” (nature and possible consequences of variants in DNA, RNA and protein; description in HGVS nomenclature) and followed by applications for robust variant classification as well as overarching topics such as the MANE project, the use of HPO terms, gene/disease specific databases and the importance of data sharing initiatives. One of the main points of the course was the presentation of the limitations of NGS diagnostics, as a lecture and workshop. Furthermore we were lucky to have speakers from the major genome browsers UCSC and Ensembl, as well as leading scientists in their field, who presented their state-of-the-art lectures and workshops and thank them for taking time to join us. Many sessions include interactive polling and problem solving, this was in most cases the starting point of lively discussions and in addition to the specific questions of the participants about the presentations, ethical issues of genome analyses were also discussed.
 

Global Variome’s mission to increase capacity is being realised through conferences and training courses such as these.  If you missed out on the live course you can still register for on-demand viewing at veptc.variome.org or signup to the mailing list to be kept informed about the next course.

We would like to sincerely thank all our speakers and participants with a special mention to our sponsor Qiagen.

We hope that you can all join us again at our next course.

The VEPTC2021 Team

 
 

 VGNC now naming pig genes | EMBL's European Bionformatics InstituteHGNC Newsletter Summer 2021


 
To view this newsletter, please visit:
https://blog.genenames.org/hgnc/2021/08/16/Summer_newsletter_2021">https://blog.genenames.org/hgnc/2021/08/16/Summer_newsletter_2021
 
If you have questions or comments on our newsletter or on any human gene 
nomenclature issue, or if you would like to unsubscribe from this 
newsletter, please email us at: hgnc@genenames.org
 
 
 
 

A paper has been written on HUGO’s history to be included in a special issue of American Journal of Medical Genetics Part A (AJMG-A) to honor Dr. McKusick's 100th birthday. Thank you to everyone who contributed.
 
The view the paper, please click here

 



EuroGEMS.org guide to online genomics resources is now available in English and Spanish
 
EuroGEMS.org - the easily-navigated guide to 110 selected international online educational genetics and genomics resources and databases, for professionals & other audiences, is now available in both English and Spanish. Created by Prof Edward Tobias on behalf of the European Society of Human Genetics (ESHG), www.EuroGEMS.org is already used in over 120 countries and is now being professionally translated into non-English-language versions. The first complete translation (into Spanish) is now being used across Spain, South America and the USA.
 
To facilitate genomics education, Ed also recently created two free massive open online courses (MOOCs), together with his colleagues at the University of Glasgow, UK. The first MOOC provides an introduction to medical genetics & genomics. The second MOOC looks in more detail at the use of genomics, databases, 3D protein structures and precision medicine in relation to clinical practice. Also, with his son, Adam Tobias, he has created a set of educational genomics smartphone apps, free on the App Stores, which include an illustrated simple guide to genomics and bioinformatic terminology and an accompanying self-assessment quiz.
 
Ed is an invited member of the HUGO, ESHGECMGG-exam and GMF-UK-Advisory-group committees for international genetics and genomics education and was the recipient of the ESHG Education Award 2021. He can be contacted atedward.tobias@glasgow.ac.uk.
 
 



LOVD integrates with MobiDetails: an online DNA variant interpreter

 
LOVD has recently integrated with MobiDetails, allowing bi-directional data transfer between the two systems. MobiDetails is an online tool that collects annotations for given variants, aiding in the classification. Assessing the effect and pathogenicity of a human DNA variant often means browsing many websites to get into the pertinent data with the risk of losing some information as some predictors can be challenging to run. In addition, one may not be willing to share personal and/or professional data with third-party companies just by using an online tool. MobiDetails is an academic tool, open-source and freely available for everyone, able to retrieve annotations for any type of small variant, such as substitutions or small insertion/deletions. Available annotations include various HGVS expressions, classical missense predictors, Clinvar and LOVD interpretations, population frequency data, but also many innovative approaches such as MetaDome, SPiP, or HexoSplice. MetaDome analyses the position of your residue of interest in the light of domain evolution. SPiP is a splicing predictor that aggregates several predictors and runs the most appropriate one depending on the variant’s position in the gene. HexoSplice may help find non-canonical splicing variants by analysing splicing regulator elements. Data is also available to interpret 3’UTR variants with 3 different predictors.
 
Registered users can define their own ACMG classification, guided by the semi-automated interpretation provided by wintervar, but also contact their peers through the application. MobiDetails is able to display which instance of LOVD reports the variants and what are the related interpretations. Moreover, it is also able to automatically submit the variants and their classifications to the LOVD Global Variome Shared instance, therefore assuring the persistence of the data. MobiDetails has been published in the European Journal of Human Genetics, and the article is available here: https://www.nature.com/articles/s41431-020-00755-z">https://www.nature.com/articles/s41431-020-00755-z. The tool itself is available here: https://mobidetails.iurc.montp.inserm.fr/MD/. There is also a Twitter account @MoBiDiC_BioInfo which keeps you updated with the latest news.
 
 
 

ISCN has been published as books and in a peer-reviewed journal since 1960. A web-based version of ISCN was introduced for the first time in 2020 (https://iscn.community.karger.com/). The web-based version is identical to the book except amendments can be made easily post publication and highlighted. A list of the addendums and errata will also be published shortly. The https://iscn.community.karger.com/ website also includes HGVS recommendations for DNA, RNA and Protein.
 
In addition, there is a Forum for geneticists to ask ISCN related questions or suggest improvements to the nomenclature. To date there have be 42 questions relating to the use of ISCN, 18 via this Forum and 24 by email. As a consequence of publicising the Forum more questions are now coming via this platform.
 
Optical genome mapping (OGM) is a technique now being used in diagnostic laboratories and a notification is currently open on the website for the genetics community to comment on some nomenclature suggestions for reporting normal and abnormal results. A working group is currently being set up discuss the OGM nomenclature.
 
ISCN allows a standard nomenclature that can be used to describe any genomic rearrangement identified either by standard karyotyping or molecular methodologies.
 
 


 

Missed GA4GH 9th Plenary?

Presentation recordings are now available on the GA4GH Youtube Channel! Click the button below to catch-up on 9th Plenary talks and panels.

https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fctkd304.na1.hubspotlinks.com%2FBtc%2F2J%2B113%2FctKd304%2FVWnw177kcfplW4XvZcW6CFPdFV9TLwZ4ykwPVN54gmP_3q90JV1-WJV7CgNqZW7GY9_12MzGR3W91qywq1_k6vkMQtsMXD9S_VW7CmjFF6cZLqqW2MsmhB8C_nTmW3KRSN-1xxrPtW3pZ7W42NWpv8W6NwJn53sLPzLW33d8-P1YCzRCW7vY5qV6gLnQVW6lCdsr59q6ZSW8Y-Mr721G9ldMyD8LdT4CdLW33v6mZ4jpgljW1p6Hs_8Wmy5HN1M5FZvLt-DKW5qrm2c6c2rzQW531qgc1hZYG4W586v4-4PkYDPW6dpJJV8S_KfrW6SHT286wvy_9W4R9rqv7gtDLWW7FrZtN82YBvyW24svdY78nFFTW5gJpFq9gZl1cW2nMYZ113hRPHW5BgZYt2ZqXKtVP9JNn27CsGk37FZ1&data=04%7C01%7Camy.mcallister%40newcastle.ac.uk%7Cd02a35a092c2437d191f08d988d376bf%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C637691264079096171%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=pXFLL3IfK9dmmEFW6PhJ7gQUWqwcGzusVCq9%2F8rOH74%3D&reserved=0">View 9th Plenary Playlist
 

 
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fctkd304.na1.hubspotlinks.com%2FBtc%2F2J%2B113%2FctKd304%2FVWnw177kcfplW4XvZcW6CFPdFV9TLwZ4ykwPVN54gmPp3q905V1-WJV7CgM0sW8xDT927x0v7dW1M9BH11bCwCtW3GVFQC7Ggq8QW2rZFhk7tN4dZW5LnF7d5WVx08W25nB9w1dJW7DW1GtyT118pt-1W6jBMYV8rTC2NW3wlwRG7KFbh4W76TFRr4bvSqqW91_b2y8wvxmsW90gbnX681gdBVkVn1_6YMVFrN8Lqgzgp50kBW138whR6X2nq3W2XtKb61P1JY3W4Xjz6q84w3yFW7TXvj26jlZJkW1k3K936vFNqtW2bRZb71bJz4CW53bzng3wCmXvW3gPJnk90QfBXW5dcWBH7wQhGKW5s5bkt8YQY4f3q651&data=04%7C01%7Camy.mcallister%40newcastle.ac.uk%7Cd02a35a092c2437d191f08d988d376bf%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C637691264079106126%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=X%2Flp59bKIa%2BUmNMDoiYynqnlm5XcwyKM8ag4Uu5HUiI%3D&reserved=0">GHIF-logo-01-1536x426-1

November 16 – 17, 2021

The GHIF aims to support the adoption of GA4GH standards and clinical implementation of genomics. Attendees will hear updates from current GHIF efforts and discuss opportunities for future collaboration.

For more information, see the event page 
 
 
 
 


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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