Blog

Proposal SVD-WG010 (var distance) is now closed. The nomenclature committee will evaluate the comments received and make a decision as soon as possible.

Thank you
On behalf of the Sequence Variant Description Working Group,
Johan den Dunnen (chair)

Tuesday August 24, we had the second one-hour online HGVS nomenclature session. People from different parts of the world joined at 3 pm (GMT) to work with HGVS nomenclature. After a short introduction, participants with different levels of experience had to answer nomenclature-based questions using the DirectPoll system. After each question, it was explained why a particular answer was correct or not. Following the online session everybody learned a bit more about applying the HGVS nomenclature recommendations in practice. Although I could not check, I don’t think a single participant answered them all correctly. At the end of the session there was time for participants to ask questions directly and discuss  nomenclature related issues.
 
While following the online session live is more attractive, it is possible to give it a try afterwards. For this, we use the Socrative platform, where you can find the questions, answers and an explanation of the correct answer. To give it a try, go to Socrative and select classroom HGVSonline2 (https://api.socrative.com/rc/vKH4rQ">https://api.socrative.com/rc/vKH4rQ). Over 200 people have tried the Q&A of the first online session, available as classroom HGVSonline.
 
Questions to be discussed next time are taken from the questions we receive daily (at VarNomen@HGVS.org). In addition, by checking the questions answered in Socrative, we get a nice overview of the parts of HGVS nomenclature which are problematic, meaning they need additional attention. If you have a question regarding HGVS nomenclature you would like to be discussed, please email!

 
Our next session will take place on Tuesday 26^th 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. 
 
 
 
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.

As part of the newly merged HUGO, we have reorganised our committee structure. One of our committees will be the HUGO Nomenclature Standards Committee, which will  promote the use of internationally developed and agreed standards in genomic research.
 
The committee is supported by several working groups, each focusing on a specific Standards topic. The currently approved working groups include:
- the HUGO Gene Nomenclature Committee (HGNC)
- the HGVS nomenclature Sequence Variant Description working group (SVD-WG)
- The ISCN Standards committee

The ISCN Standing Committee welcomes an inclusion of a representative on the HUGO Nomenclature Standards Committee. For more information on the ISCN Standards committee, please click here 

LOVD security improved by hackers

Not all hackers are bad. In fact, there are large groups of so-called "white hat hackers" that attempt to break into online systems not to cause damage, but to report vulnerabilities to their owners. Often these white hat hackers are rewarded small "bounties", either gifts or financial compensations for their efforts. A large majority of white hat hackers are from developing countries and use these bounties to fund their studies. This July, LOVD sent out an invitation (a "bug bounty program") which caused some 15 white hat hackers to scan LOVD and the LOVD website for vulnerabilities. Several small issues were found, as well as two vulnerabilities that attackers could potentially use to set up a successful breach of LOVD security. Although no breach had actually occurred, all vulnerabilities were fixed and everyone who reported an issue received financial compensation.

DECIPHER v11.6 Released 

You can also view this on the web at:https://www.deciphergenomics.org/about/news

It is now possible to query Matchmaker Exchange through DECIPHER to find matches for small copy-number variants that overlap a gene, in addition to sequence variants. Matchmaker exchange allows the federated discovery of potential matching patients in connected databases. DECIPHER currently supports the searching for patient matches in PhenomeCentral, MyGene2, GeneMatcher, RD-Connect and Broad-seqr. When DECIPHER users query Matchmaker Exchange, overlapping phenotypes are now highlighted in the interface to enable relevant patient matches to more easily be identified.

On plots of individual patients' height, weight, and head circumference (visible to depositors who enter this information), the points representing individual observations are now connected with curves instead of lines, to better approximate the likely pattern of growth.

The genome browser tracks menu has been updated so that the available tracks are grouped to allow users to more easily find tracks of interest. The tracks menu can be accessed by clicking on the word "Tracks" in the top left of the genome browser.

It is now possible for DECIPHER depositors to copy a patient's phenotypes and associated HPO codes. Click on "Show simple term list" to view this information (this is only visible for patients in your own projects). This development helps enable interfacing with electronic health records and family tree programs.

BRCA Exchange Release 50

We are excited to announce that Release 50 of BRCA Exchange will soon be live with more than 67K variants!!! Thanks to our collaboration with the ENIGMA Consortium, this release offers new data on laboratory functional assays. We anticipate that this release will go live in roughly two weeks.
 
Like recipes for chefs, functional assays are standardized processes that laboratory-based researchers use as their common language. Researchers use assays to measure and discuss how much a variant impacts “normal” biological function at a molecular level. This is why functional assays are considered a rich source of information that can help people understand and manage their potential genetic risk for cancer.
 
We want to give a shout out to the many people who contributed so much work and thought to this functionality, especially team members Michael Parsons and Zack Fischmann. #heritablecancer #knowyourrisk #BRCA  
 

The Global Alliance for Genomics and Health (GA4GH) has approved a policy for the return of clinically actionable genomic research results, the first such policy approved by an international body. Click here for more information.

Earlybird registration ends 19th of July so register now to make a saving!

This year the course will be an immersive virtual experience and will take place from the 21st to the 23rd of September 2021.  Core topics will be delivered live with ample opportunity for Q & A; some topics will be on-demand.  

Participants will have access to recordings after the course.

Expected Participants are people working in a DNA laboratory including clinical diagnostic labs involved in DNA sequencing data analysis.

VEPTC 2021 will be a fully immersive virtual event using the Attendify platform.
 

The course will include:

• Variants in the genome, position & possible consequences
• NGS: what method to apply (gene panel, WES or WGS) and where technology fails
• NGS limitations: sequencing technologies / calling variants (SNV+CNV+SV)
• CNV calling/ analysis: applications and challenges
• SNV calling/ analysis: applications and challenges
• HGVS Nomenclature; describing variants
• Human Phenotype Ontology (HPO)
• Integration of phenotypic and genomic data to diagnose patients with rare diseases 
• Annotating variants
• Variant Classification (ACMG recs.)
• Prediction tools
• Ensembl Genome Browser
• UCSC Genome Browser
• Future developments
• Qiagen variant interpretation workshop
• & more…

VIEW THE PROGRAM HERE: https://veptc.variome.org/program.html 

We invite you to register, and submit an abstract for consideration as a virtual poster (only if you wish) and look forward to your participation.  

REGISTER HERE: https://veptc.variome.org/registration.html

Further details about the event may be found on the website:  veptc.variome.org

For more information, see the event page