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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.

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GV Newsletter - August 2021



We are now formally sharing the news that the 25th Human Genome Meeting has been postponed to 23-25 May 2022, due to the COVID-19 pandemic.
 
More information, please visit: https://www.hugo-hgm2022.org/
 
 

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


Click here to view the proposal
 
Thank you
On behalf of the Sequence Variant Description Working Group,
Johan den Dunnen (chair)
 


HGVS nomenclature Q&A sessions (by Johan den Dunnen)

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 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. 
 
 
 
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 DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources

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  
 
 
GA4GH

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.
 
13th Conference of the AfSHG & 1st Conference of the Tanzania Society of Human Genetics
Dar es Salaam, Tanzania • August 30 - September 5
For more information, see the event page
 
Harnessing biological data: from molecular
processes to human health
Basel, Switzerland • September 13 - 15
For more information, see the event page
 
The VIII International Conference of Cardiovascular Genomic Medicine Tickets, Thu 16 Sep 2021 at 12:00 | Eventbrite

For more information, click here  

For the the agenda,  click here

 
 


The 5th Variant Effect Prediction Training Course
is open for registration!
 
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
 
8th International Workshop on ​Genome
Privacy and Security (GenoPri'21)
Virtual • September 22
For more information, see the event page
 
20th Precision Medicine World Conference (PMWC)
Pittsburgh, USA • September 23 - 24
For more information, see the event page
 

GA4GH 9th Plenary

registration is now open!


GA4GH 9th Plenary will be held virtually on September 28–29. We are excited to continue engaging our global community in advancing data sharing for the benefit of human health and medicine. GA4GH 9th Plenary is a free event and, as always, open to the public.
 
For more information, see the event page
 
6th International Virtual G2MC Conference
Virtual • September 29
For more information, see the event page
 
2021 Conference on Precision Psychiatry
Virtual • September 30 - October 1
For more information, see the event page
 


We go virtual in 2021! EHTG's 5th Meeting was cancelled because of the Covid-19 pandemic. This year we are back and will host our annual Meeting on October 8 and 9 2021 as an online congress
 
You can already register for the event or become a member and enjoy complimentary registration for the meeting. Abstract submission is now open.
 
 
Next Generation Sequencing Bioinformatics
Virtual • October 18 - 22
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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Twitter
Website
Email
 
 
 







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GV Newsletter - July 2021

https://mailchi.mp/6d44df00cc88/hugo-newsletter-april-4928346?e=93495c83ac

 


We are now formally sharing the news that the 25th Human Genome Meeting has been postponed to 23-25 May 2022, due to the COVID-19 pandemic.
 
More information, please visit: https://www.hugo-hgm2022.org/
 
 


Proposal SVD-WG010 (var distance) is now open for Community Consultation. You are invited to review and comment on this proposal.  
 
Click here to view the proposal

 
Deadline for comments - Friday 30th July- comments to VarNomen@HGVS.org">VarNomen@HGVS.org

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


HGVS nomenclature Q&A sessions have started!
 
On June 22, we started an experiment, an online HGVS nomenclature session. We thank those who dared to attend the first session; there is always the danger of technical issues. But not this time, everything went smoothly. We had a mix of experienced users and nomenclature beginners who enjoyed the chance to practice and discuss relevant nomenclature issues.
 
The session started with a brief welcome from Johan den Dunnen, chair of the HGVS nomenclature committee. Next, were a series of prepared questions for the participants to answer using the DirectPoll system. Participants were able to see each other’s answers anonymously. After each question, the answers were revealed and explained. Was it easy? Certainly not. One question in particular was answered incorrectly by all, even from the experienced users of the group. But this is why we wanted to hold these sessions, giving people a chance to practice and discuss in a safe environment. After the prepared questions, there was time for participants to ask specific questions directly.
 
For those interested to give it a try, the Q&A session is available using Socrative, classroom HGVSonline (https://api.socrative.com/rc/ibPQGW).
 
 
Our next session will take place on Tuesday 24th August, at 3pm 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.
 
 

 

UNESCO Online Database Training Course

Financially supported by a grant from UNESCO, Global Variome is organising an "Online training course in curation of human gene/disease databases". Interested students from all over the world applied earlier this year. A Global Variome committee has now selected the 16 participants that are allowed to enter the course. Selected participants come from 12 different countries: Argentina, Cameroon, Egypt, Ethiopia, India, Malaysia, Mexico, Nigeria, Romania, Senegal, Turkey and South Africa.
 
The online training sessions will be held on Mondays over the next few months. To accommodate the 13-hour time difference between the participant's home countries, there will be alternating morning and afternoon sessions (based on UTC). Sessions will be recorded and made available for the participants who are unable to join. Between sessions participants will have to complete specific tasks focussing on a gene/disease they have selected. At the end of the course the participants will be curator for one of the genes in the "Global Variome shared LOVD" (http://databases.lovd.nl/shared">http://databases.lovd.nl/shared). The first session will start July 19, 8 am (UTC).
 
SVD-WG: thank you Donna Maglott!

Donna MaglottThe HGVS nomenclature committee, the Sequence Variant Description working group (SVD-WG), is a group of experts guarding the nomenclature recommendations. The committee currently exists of eight members and three observers (representing HGVS, GV/HVP and HUGO). Until now, membership of the committee has been assigned on an ad-hoc basis. The plan is to make membership of the HGVS nomenclature committee a more open process where candidates apply for membership and committee members serve a specified term time. The plan is to start this process
later in the year, under the umbrella of the new HUGO, where the three organisations supporting the HGVS nomenclature have started to collaborate more closely.
 
Donna Maglott (NCBI) has recently decided to step down as a member of the SVD-WG. Donna will be replaced by Terence Murphy (NCBI). From the start, Donna has been a very active and responsive member of the SVD-WG. Her input, expertise, commitment to standards, spirit of collaboration and the discussions within the committee have always been appreciated. Donna made essential contributions to the HGVS nomenclature recommendations as they are now. These recommendations are not perfect, they will probably never be, but they are of very high quality, serve a need and this is why they are applied as THE standard world-wide, especially in a diagnostic setting. Donna can be proud on having played an essential role towards this achievement.
 
Donna, on behalf of the SVD-WG, thank you very much, enjoy your well-deserved retirement!
 
 

File:Flag map of the United Arab Emirates.svg - Wikimedia CommonsUAE launches new Centre for Genomic Discovery
 

"The UAE has launched a 'first-of-its-kind' Centre for Genomic Discovery, which will help diagnose and treat patients with genetic disorders as well enhance local genomic research and train the country’s next generation of scientists"


For more information, click here 
 


"In response to the global COVID-19 pandemic, we are no able to organize the traditional conference and celebrate all together the 20th Gene Forum"

"This year's presentations will cover themes from the use of genomic data in personalized medicine and applications in healthcare, pharmacogenomics, regulatory genomics and molecular functions, population genomics and human microbiome interactions. Given the situation in the world, this year's Gene Forum will also have a session on COVID-19 research."
 
For more information, see the event page
 
 
BC2

Harnessing biological data: from molecular processes to human health


[BC]2 Basel Computational Biology Conference
13 – 15 September 2021
Congress Center Basel, Basel, CH


Early bird registration now open! 

For more information, see the event page 
 
 


The 5th Variant Effect Prediction Training Course
is open for registration!
 
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
 
 
 

GA4GH 9th Plenary

registration is now open!


GA4GH 9th Plenary will be held virtually on September 28–29. We are excited to continue engaging our global community in advancing data sharing for the benefit of human health and medicine. GA4GH 9th Plenary is a free event and, as always, open to the public.
 
For more information, see the event page
 


We go virtual in 2021! EHTG's 5th Meeting was cancelled because of the Covid-19 pandemic. This year we are back and will host our annual Meeting on October 8 and 9 2021 as an online congress
 
You can already register for the event or become a member and enjoy complimentary registration for the meeting. Abstract submission is now open.
 
 
 
 


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)
 
 
Facebook
Twitter
Website
Email
 
 
 







This email was sent to amy@variome.org 
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Human Variome Project · Centre for Life · Times Square · Newcastle Upon Tyne, Tyne and Wear NE1 4EP · United Kingdom 

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GV Newsletter - June 2021


https://twitter.com/humangenomeorg/status/1400363296725819392
 
Complete Human Genome Sequence

New Scientist Default Image
On June 26, 2000, the draft human genome sequence was announced. 21 years later, on May 27, 2021, the Telomere-to-Telomere (T2T) consortium has completed the human genome sequence! The remaining 8% of missing genetic data was added, capping the full sequence at 3.055Bbp!

Read the fill article here:
https://www.biorxiv.org/content/10.1101/2021.05.26.445798v1
 
 


NEW - HGVS nomenclature Q&A session
 
We receive a lot of questions regarding HGVS nomenclature. Currently, these questions are all answered by private e-mail, with some examples published on the nomenclature Facebook page

In order for users to gain real practical experience carrying out nomenclature tasks, we are going to try something NEW:
 
.
 
            bi-monthly online HGVS nomenclature Q&A sessions
 
The first meeting will take place on June 22, 8:00am GMT (check your own time zone here)
 
The meetings will be bi-monthly, on the 4th Tuesday of every 2nd month (even months). We will alternate the time of the meeting in order to allow people from either Asia+Australia, Europe+Africa or North+South America to follow the meeting during the day. We plan to record the meeting for those not able to join.
 
Meetings will take 60 minutes and have a standard format:
1) Short welcome (5 min)
2) Participants answer questions (35 min)
3) Questions from participants (15 min)
4) Close of meeting

For questions to be answered by participants we will use an online polling system (DirectPoll).  Questions 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'.
 
 
For HUGO members, participation will be free. Details for non-members to join will be shared later. To register your interest, please contact amy@variome.org
 
Interested to support the HGVS nomenclature work? Please consider sponsoring one of the bi-monthly meetings. For details, please contact amy@variome.org. Of course, we will acknowledge sponsorship in advertisement and during the meeting.

 
 


For more info click here
 
 


It's not too late to sign up to our Scientific Conference: Data Insights in a Pandemic. Taking place on 23rd June, the #HDRSciCon will be an exciting full day virtual event showcasing the latest advancements in health data science. 

 
 
 
https://www.ivvy.com.au/campaign/link/process/id/6e7fd0cc6cedef3f9014ed9e963270da/s/9c7b38a1e5345caad81d3f21e989566a/account/613/report/56626">VEPTC 2021 IMAGE
https://www.ivvy.com.au/campaign/link/process/id/6e7fd0cc6cedef3f9014ed9e963270da/s/9c7b38a1e5345caad81d3f21e989566a/account/613/report/56626">VEPTC2021 image

Don't miss your opportunity to learn - attend VEPTC 2021!

We are excited to announce that the next Variant Effect Prediction Training Course is now open for registration!

This year the course will be an immersive virtual experience and will take place from the 21st to the 23rd of Sept. 2021.  Core topics will be delivered live with ample opportunity for Q & A; some topics will be on-demand.  We invite you to register, and submit an abstract for consideration as a virtual poster (if you wish) and look forward to your participation.   

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

To find out more please visit the website.
 

...
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Posted by on in Press Releases
GV Newsletter - April 2021



Last month, we held our 1st HUGO Executive Board meeting, combining the efforts of HUGO, HGVS and HVP into one merged organisation! 

 
 


The deadline for the Online training course in curation of
human/gene/disease databases has passed!

We received an incredible 32 applications from all over the world for a 16 participant course. These applications are currently with our Select Committee.

Thank you applicants, you will be notified of the outcome in June!

        
 


NEW - HGVS nomenclature Q&A session
 
We receive a lot of questions regarding HGVS nomenclature. Currently, these questions are all answered by private e-mail, with some examples published on the nomenclature Facebook page

In order for users to gain real practical experience carrying out nomenclature tasks, we are going to try something NEW:
 
.
 
            bi-monthly online HGVS nomenclature Q&A sessions
 
The first meeting will take place on June 22, 8:00am GMT (check your own time zone here)
 
The meetings will be bi-monthly, on the 4th Tuesday of every 2nd month (even months). We will alternate the time of the meeting in order to allow people from either Asia+Australia, Europe+Africa or North+South America to follow the meeting during the day. We plan to record the meeting for those not able to join.
 
Meetings will take 60 minutes and have a standard format:
1) Short welcome (5 min)
2) Participants answer questions (35 min)
3) Questions from participants (15 min)
4) Close of meeting

For questions to be answered by participants we will use an online polling system (DirectPoll).  Questions 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'.
 
 
For HUGO members, participation will be free. Details for non-members to join will be shared later. To register your interest, please contact amy@variome.org
 
Interested to support the HGVS nomenclature work? Please consider sponsoring one of the bi-monthly meetings. For details, please contact amy@variome.org. Of course, we will acknowledge sponsorship in advertisement and during the meeting.

 
 
BRCA Exchange is thrilled to announce that gnomAD 3.1 will be part of our next release!   We have integrated the gnomAD 3.1 non-cancer subset, which contains whole-genome data from more than 74,023 ethnically-diverse samples, and increases the BRCA Exchange variant count by 25,406 BRCA variants to 65,822 variants altogether!  Moreover, this globally-diverse population dataset is a rich source of information for variant interpretation.  We are currently working with the ENIGMA and ClinGen consortia to leverage these data for variant interpretation, and anticipate that they will lead to the expert curation of tens of thousands of unclassified BRCA variants. 
 
 

InSiGHT awarded funding from the NIH through ClinGen/ClinVar to support the Variant Interpretation Committee around the world, which is now the ClinGen Variant Classification Expert Panel (VCEP) for Colorectal Cancer & Polyposis, so covering MMR, APC, MUTYH, POLD1/E, & hamartomatous genes.
 
The InSiGHT DNA Database Governance Committee has transitioned, with new members Ian Frayling and Gabriel Capella (both InSiGHT Councillors), Marc Greenblatt, Stefan Aretz (each InSIGHT members). Rolf Sijmons continues as a member. Finlay Macrae is the Councillor responsible ex officio and JohnPaul Plazzer the overall curator of the databases.  We are grateful for the wise council of Muarizio Genuardi and Mike Woods who have retired from their roles as members of this committee.
 
 InSiGHT's Variant Interpretation Committee has morphed into, and with, ClinGen as the ClinGen InSiGHT Variant Curation Expert Panel (VCEP). There are several subVCEPs within this, covering the genes of major interest in hereditary colorectal cancer: the mismatch repair genes, APC, MUTYH, STK11, BMPR1A, SMAD4, POLE, and POLD1. The MMR InSIGHT VCEP is well established and accepted by ClinGen for its work in curation of the MMR genes. The invitation from NIH to support the curation of the less developed genes (with respect to curation) was addressed by InSiGHT in a proposal lead by InSiGHT members Marc Greenblatt and Matt Ferber. This covered all the non MMR genes listed above and of interest to InSIGHT. It was successful!
 
 The grant will cover work by John Paul Plazzer, other new biocurators, and administration. The curation will be rolled out progressively. Already there are regular fortnightly meetings being held relating to APC, through the chairmanship of Stefan Aretz (Germany) and supported by Deb Ritter in USA.  Elke Holinski Feder remains chair of the MMR VCEP, supported by Andreas Laner in Munich which meets regularly also.  Addressing discordant pathogenicity assertions as registered on the ClinVar (USA NIH) database is a high priority and the challenges of applying the ACMG framework for curation of genes to the specific genes under attention, are major components of ongoing work.
 
Special recognition of medical and genomic health students Lachlan O'Connor, Matt Daly, Sherry Yin, Varun Kaushik and Marissa Rose has been instituted by InSiGHT Council. Sherry continues as an active biocurator for APC variants.
 
 
 
Clinical DNA Variant Interpretation - 1st Edition - ISBN: 9780128205198, 9780128205204
I am proud to share with you a recent book publication,
"Clinical DNA Variant Interpretation: Theory and Practice"

Congratulations to those HVP ISAC members
who wrote chapters in the book! 
 
https://www.elsevier.com/books/clinical-dna-variant-interpretation/lazaro/978-0-12-820519-8
 


Visit Event Page
 
 

   Curating the Clinical Genome (Virtual Conference)

   May 12th - 14th 2021

   Wellcome Genome Campus, UK 

   The conference will bring together the clinical genomics and biodata community to discuss best               practices for the clinical use of genomic data, including interpretation and clinical utility, and the consensus generation of curated knowledge. This is latest in the series of meetings on this topic, which have been spearheaded by the ClinGen and DECIPHER consortia.
   
 

IHCC 4th International Cohorts Summit: May 25-27, 2021

Modern connection technologies background . Mixed media

IHCC members are invited to save the dates for the 4th International Cohorts Summit of global leaders of large-scale longitudinal cohorts on Tuesday, May 25 through Thursday, May 27, 2021 hosted by the International HundredK+ Cohorts Consortium (IHCC). This virtual event follows the May 2020 3rd International Cohorts Summit and will build upon the strategic planning initiative kicked-off at the IHCC Members Workshop in November 2020. 


Visit Event Page
 
ICGC ARGO

Due to the ongoing COVID-19 pandemic and restrictions currently imposed the International Cancer Genome Consortium 17th Scientific Workshop / 4th ARGO Meeting will take place virtual from the 14th - 15th May 2021 and will be hosted from Peking University, Beijing, China.

Visit Event Page
 

Cancer Genomics & Haematological Disorders Conference:
June 8-11, 2021

Dear Healthcare Professionals,

On behalf of Newcastle University and Members of Malaysian Laboratory Haematology Society (MMLHS), it is our great honor and pleasure to invite all of you to a virtual seminar entitled Cancer Genomics & Haematological Disorders  which will be on June 8th to 11th, 2021. With the health and safety of all participants being our topmost priority, this online course would be the best solution for all of us.

Register now and the secretariat will soon send you detailed information on the webinar. Looking forward for your participation in this virtual seminar.

Thank you.

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GV Newsletter - February 2021

 

As you know back in 2016, and after the death of Dick Cotton, we moved the HVP office from Melbourne and formed a UK charity under the name Global Variome. For the last 18 months we have been in talks with HUGO over a potential merger between HVP, HUGO and HGVS. I am pleased to tell you that we are in the final stages and are planning to pilot the new merged organisation over the next year.  

As a member of HVP, this merger should cause little disruption to the great work you are doing.

With this new merger, we plan to combine our HVP committees; for those interested in maintaining their membership with the Human Variome Project, we hope that you will join this new group. Our goal is the same; to maintain an international network of individuals and industry to ensure that all genetic variation information can be collected, curated, interpreted and shared for the benefit of human health. 

We will operate under the collective membership of HUGO. Members will be invited to associate with HVP and/or HGVS, each of which will have dedicated committees within the structure and have seats on the executive board. We will have a dedicated section in the Human Genome Meeting.  The Global Variome will retain its separate identity as an associate NGO of UNESCO and will facilitate educational activities there.  

We will share further details as they become available.  If you have questions please contact us via email to amy@variome.org

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*CALL FOR PARTICIPANTS* - Online training course in curation of human gene/disease databases

16760192

 

*CALL FOR PARTICIPANTS*

Online training course in curation of human gene/disease databases

(supported by Global Variome and the UNESCO 2020-2021 Participation Programme)

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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. 

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We would appreciate your input... 



Proposal SVD-WG009 (conversion) is now open for Community Consultation. You are invited to review and comment on this proposal.  
 

Click here to view the proposal
 


Deadline for comments - October 31st 2020 - comments to varnomen@variome.org 

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

 

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PUBLISHED - Quality Assessment Criteria for Variation Databases

 

Click here to view the paper 

 

These guidelines have now been published on the HVP website. 


We encourage all memebers to:
1. Circulate it to their colleagues and students
2. Post on their web-site
3. Suggest the guide be used as a basis for discussion at up-coming meetings

This paper is the result of the work of many HVP members and we thank them very much – in particular the authors, Mauno Vihinen and John Hancock

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GV/ HVP Newsletter - August 2019
 
 


The Community Consultation call for proposal SVD-WG008 (RefSeq) has been open since 20th July and will close on Monday 30th September 2019. The proposal suggests to extend the HGVS recommendations by specifying what sequences can be used as a reference sequence. See http://varnomen.hgvs.org/bg-material/consultation/svd-wg008/.
 
A sequence variant is defined in the context of a reference sequence which must be referred to by means of a unique sequence identifier. Because a reference sequence defines the numbering system and default state of a sequence (e.g. coding transcript, non-coding transcript), reference sequences have to follow specific requirements which seem "obvious" but were not yet defined. This proposal lists all the essential requirements.
 
Whether your opinion is positive or negative, we would appreciate your honest opinion. Please email any comments or suggestions to Varnomen@variome.org with the Subject: SVD-WG008.
 
If you would like to be on the community consultation e-mail list, please register with the GV office: amy@variome.org - Subject: SVD-WG discussion list
 

 

Meeting report: the 2019 Human Genome Meeting (HGM2019) of the Human Genome Organization (HUGO) was held in Seoul, Korea, from 24 to 26 April 2019, at Ewha Woman’s University.
 

 




Describing exon deletions/duplications
 
During the last "Variant Effect Prediction Training Course" (May 29-31, Moscow, Russia) the importance of correctly describing the variants detected using HGVS nomenclature was discussed extensively. One of the examples covered was the description of MLPA-detected deletions/duplications, many struggle with this. During the course the "Reading Frame Checker", offered per gene by the "Global Variome shared LOVD" (https://databases.lovd.nl/shared/), was pointed out as a useful support tool. The reading frame checker can be used to check the predicted consequences of a deletion or duplication of one or more exons being "in frame" or "out of frame". The reading frame checker also gave exon-based variant descriptions but these unfortunately did not follow HGVS recommendations. Since modification according to the developer was "simple" and modification should not take "more than a month" the LOVD-team left with the promise to modify the tool. Modification has now been completed and the GVsharedLOVD can be used to generate HGVS compliant exon deletion/duplication variant description like c.(93+1_94-1)_(649+1_650-1)del.
 
 


The BRCA Challenge and ENIGMA consortia are pleased to announce the publication of "Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants", Hum Mutat. 2019 Jul 11. This paper reports on the results of the CAGI5 ENIGMA challenge for predicting the clinical significance of BRCA variants.  In this challenge, six teams predicted the clinical significance of 326 BRCA variants, which had recently been interpreted by ENIGMA but for which the interpretations were not yet published.  The six teams submitted predictions from fourteen methods, which were then assessed through comparison with the unpublished interpretation.  The best performance was achieved by the LEAP methods by Color Genomics.  These methods were able to successfully leverage private information, including an internal database of genetic testing results and a subscription to HGMD.  While the results of this experiment yielded many lessons for the scientific community, the biggest lesson is that there is still private information that is valuable in variant interpretation.  To the extent that such information can be made public, science will benefit, as will genetic testing patients by extension.
 

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Professor Sue Povey - Memorial Symposium

For those of you who were unable to attend the Symposium held for Sue Povey on Friday 12th July, please see the following link:

https://www.ucl.ac.uk/biosciences/news/2019/jul/sue-povey-memorial-symposium

Within the article, you will find a collection of photos of the event as well as a copy of the ‘slide show’ of Sue that was shown throughout the day. 

Sue was a great friend and supporter of the Human Variome Project. She will be dearly missed.

 

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PUBLISHED: Ethics Checklist for Database Curators and Submitters

Click here to view the paper

We encourage all members to:
1. Circulate it to their colleagues and students
2. Post on their web-site
3. Suggest the guide be used as a basis for discussion at up-coming national meetings and local workshops

 

The paper has also appeared online at Human Mutation. PDF not available here as of yet. 

https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23881.

Click here to view the paper

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Newsletter - May 2019

https://gallery.mailchimp.com/0634203d6f80b6aabccbff98e/images/155075cb-8c7d-43fe-a04f-3cbe4734a392.jpg

 
 
 

https://gallery.mailchimp.com/0634203d6f80b6aabccbff98e/images/b96209ac-f61f-486a-b47e-dd0c6de72757.png

MEETING REPORT


“Genomic Education and Training for Healthcare”; sponsored by the ‘Global Consortium for Genomic Education (GC4GE)’, The Genomic Medicine Foundation, UK (www.genomicmedicine.org ); Convener: Professor Dhavendra Kumar; CEO & Medical Director- The Genomic Medicine Foundation (UK).

This workshop was held on 24th April 2019, at the Human Genome Meeting 2019, Seoul, South Korea. Aims and objectives included-

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Consortium Update - March 2019

 

Plase find the link to our latest newsletter here:

https://mailchi.mp/275f0115a780/gc6jdli57c

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HGVS nomenclature course @ HGM2019

 

 
title
 

                Seoul, South Korea - Wednesday 24 April 2019


 

Interested in HGVS nomenclature? Want to learn the basics? Want to increase your knowledge? Wiling to test your skills in describing variants?

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Consortium Update - July 2018
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GG2020 2018 Conference -
Precision Medicine in Thalassaemia
7th & 8th July 2018  Penang, Malaysia. 

GG2020 2020 Challenge has been making great progress in recent months. There are two important achievements to report.

First is the recent successful meeting of members held in Penang Malaysia in early July. This international meeting profiled what was happening in different parts of the world with several keynote presentations from key partners to the project, including Prof Sir John Burn, Dr Carsten Lederer from CING Cyprus and Dr Michael Angastiniotis CMO from TIF. Topics covered included addressing needs of patients in low resource settings, complexities of genotype and phenotype linking,  the challenge of incorporating precision medicine into haemoglobinopathies. The full program can be reviewed on the GG2020 website and the presenters slides are available – click here 
 
The team from Malaysia, led by Professor Zilfalil bin Alwi, who heads the Malaysian Country Node and it Co-chair of GG2020, are to be congratulated on organizing these quality meetings.
Delegates stayed on to participate in the annual meeting of the Malaysian Society of Human Genetics and the ASEAN Biomolecular Society meeting.
 
Second is to report that GG2020 Challenge has received funding for three years for a project to expand and ‘internationalise’ the ITHANET database and portal. This database forms the core of GG2020 activities and is based at CING in Cyprus. Following the establishment of an international expert panel to provide formal input to ClinGen on haemoglobinopathies as part of GG20202, it has become increasingly necessary to fund this work and expand the team who curates ITHANET.  Those wanting the know more about this should contact Petros Kountouris who is leading the project - petrosk@cing.ac.cy  - we thank the Cyprus Research Promotion Foundation who has provide the funding. Partners to the project are looking forward to three more years of successful work!

Blockchain – heard about it? Interested in it?  

In recent months, members of the Gene and Disease Locus Specific Database Council (GDLSC) of Global Variome have been sharing knowledge on this new technology and debating its utility for variant databases.  This is a call for anyone interested in following this topic and being linked up to a few others who are tracking developments. If you are interested in being part of the group to monitor blockchain technologies, discuss and occasionally report back to HVP members and Councils – please contact Helen Robinson – hmro@unimelb.edu.au
 

You may be aware that LOVD is undergoing some organizational changes to ensure its sustainability and will be moving under the auspices of the HVP (Human Variome Project).  As part of this, we are planning to form a user group aimed at involving LOVD users more directly in its development whilst providing more training and support for users.  The use of LOVD has once again grown rapidly in the past year with many more users, so it seems a good time to do this.

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Consortium Update - April 2018
 
 

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HGVS nomenclature course @ ESHG 2018

 

WebsiteEmail
 
 
 
 
title
 

                Milan, Friday June 15, 2018

with the kind support of the European Society of Human Genetics

 

Background

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HVP @ Human Genome Meeting 2018, Yokohama

HVP will offer several important sessions at HuGO 2018 in Yokohama.  The speakers have been selected to profile what is currently happening in international variant information sharing, with emphasis on projects which are making great strides in resolving the practical issues in order to accelerate progress in all parts of the world. Different aspects have been highlighted including: the need for standardized approaches to describe and share variants; the practical case for sharing global knowledge - BRCA Exchange – is explained together with further local examples; the case for equitable use of genomics in clinical practice and the implications for ensuring knowledge of the context of diverse populations; how an approach to haemoglobinopathies can provide an example for promoting the use of genomic techniques in low and middle income countries for better health outcomes; and how the BRCA Exchange is helping to highlight the need for better quality genomic variant databases required for improved interpretation.

 

See program of HVP sessions below... 

HGMprogramblog1

HGMprogramblog3

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Consortium Update - February 2018
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HVP Shared Database

 
Last year saw a considerable increase in the use of LOVD databases (numbers for Leiden/HVP hosted installations only):

  • The number of monthly page views increased from approximately 350,000 to almost 450,000 with the number of unique monthly visitors (each institute counted as one visitor) increased by 20,000.
  • The use of LOVD, api, computer requests for information increased from 4,000,000 to >39,000,000.

Statistics for the HVP shared gene variant database show a substantial increase as well:

  • The number of submitters, people actively sharing data with the HVP database, has grown in 2017 from 1046 to 1431.
  • The total number of variants in the database increased from 377,974 (49,238 unique) to 549,140 (79,224 unique), the number of individuals for which data were shared from 156,577 to 285,424

 
Total numbers (# installations, # individuals, # variants) for all public LOVD installations can be found on the LOVD website (http://www.lovd.nl/3.0/public_list)
 
Impressive numbers! We would like to thank all the LOVD team and it’s users for all their hard work.
 

 

        

 
A great start to 2018 as Dutch data now being shared with LOVD. Some time ago, the 9 Dutch clinical labs decided to share all classified variants which each other. They have now made an even bigger step and shared this data with the world. 

The project was initiated by the (Vereniging Klinisch Genetische Laboratoriumdiagnostiek, http://www.vkgl.nl), the Dutch association of laboratories for Clinical Genetics. Headed by Dr. Marielle van Gijn (UMC, Utrecht), the project first collected the data in a national repository built on Molgenis software, and checked whether variant classifications between labs agreed. 

The Dutch database currently contains over 90,000 classified variants. The variants for which there was consensus, roughly 28,000 classifications (>10,000 unique), have now been shared with the HVP shared database (LOVD). The variants can be found at https://databases.lovd.nl/shared, go to the Variants tab, select top option (View all genomic variants) and query for Owner "VKGL" (last column on the right). Soon all variants will be publically shared with both the HVP shared and ClinVar database.Our compliments and congratulations to the Dutch initiative. Which country is next?
    
 

ESHG, Milan 2018 - HGVS Nomenclature Course


Friday June 15, Milan (Italy)
Teach the Teacher:  HGVS nomenclature
 

A course on HGVS nomenclature, organised with financial support of the European Society of Human Genetics (ESHG), in collaboration with the Human Variome Project (HVP and the ESHG Education Committee.

HGVS nomenclature, currently supported by the HGVS, HVP, HUGO and GA4GH, is the language by which diagnostic reports as well as scientific reports on human genetic variation are drafted. Understanding this language and knowing how to use it is crucial for mutual understanding between geneticists and for the accuracy of diagnostic and scientific reporting in Human and Medical Genetics. A correct use of the HGVS recommendations prevents miscommunication and ensures that variants can be efficiently retrieved from existing data repositories facilitating variant annotation and classification.
The aim of the course is to give participants a detailed overview of the HGVS nomenclature. i.e. the recommendations for the description of sequence variants (Den Dunnen et al., 2017, Hum.Mutat. 37:564,;http://varnomen.HGVS.org). The course will have a “Teach the Teacher” format, i.e. after the course participants should be able to teach HGVS nomenclature to others. Registration to the course is free, but limited to 16-20 participants. Participants will be selected based on their willingness to act as a local (national) teacher and their expertise in the field. In addition we want to make sure participants are spread internationally, covering all continents on the globe. 

The entire course will be recorded (sound and video) and used to develop educational tools on HGVS nomenclature, including an e-learning module.

To register, please send a letter (max. A4) with your contact details and your motivation
ultimately April 15, 2018  to:

    ESHG Education Committee
        att. Johan den Dunnen

    VarNomen@HGVS.org

    Subject: HGVS course

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Message from the Executive Chairman - Dec 2017

Merry Christmas

 

Dear All

Firstly, I would like to take the opportunity to thank all HVP members for their contributions over the course of 2017. It has been a big year for us. As you know, it has been just over a year since I took over as Chair of the GV Board and during that time, there has been a lot of activity. We have seen open and transparent data sharing take off internationally, with substantially more interest in the core business of areas of HVP.

In particular, I would like to acknowledge the members of the various Councils of HVP – International Scientific Advisory Committee (ISAC), Gene/Disease Specific Database Advisory Council (G/DSDBAC) and International Confederation of Countries Advisory Council (ICCAC). Together with the Global Variome Board, these individuals make a valuable contribution to the work of HVP. Our achievements are the result of the work done by many of you who are based in research institutes, academic bodies, laboratories and the like. Linking up our activities and learning from each other underpins the progress of HVP.

 Discussions are continuing to align the LOVD databases, run by Johan den Dunnen, with the data centre under construction to support Genomics England. Johan has been very active leading our outreach and educational programmes. Activities this year have included the very successful academic meeting in Santiago de Compostela, a 3Gb training course in Mexico City and a well-supported Variant Interpretation training meeting in Prague. In 2018, we will seek to align our programme with the activities of the European Society of Human Genetics (ESHG) and organise another Variant Interpretation meeting in the East, possibly taking advantage of the Newcastle Medical Faculty facilities in southern Malaysia, adjacent to the Singapore border, offering excellent international travel links.

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Consortium Update - November 2017
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Ethics Checklist – comments please

HVP’s Gene/Disease Specific Database Advisory Council (GDDAC) has been working on an Ethical Checklist to assist database curators and it is time for it to go to member comment. Checklist For Gene/Disease Specific Database Curators To Enable Ethical Data Management  can be viewed here (LINK) – once approved, this will become an addition to HVP’s growing set of official Standards and Guidelines that assist members. This Checklist is an up-dated version of 2010 guidelines and the checklist format is designed to ease implementation because after all, it is the implementation that is most important – there is little point in having guidelines if they are not easy to use. The Checklist is posted here until 1 February 2018 for comment. We are looking for two types of comment:

  1. Comments on the content
  2. Comments and suggestions of how the final version can be implemented – how could you use this in your area?

Please send any comments to Helen Robinson hmro@unimelb.edu.au
For  more technical issues please contact the leader of the working group who oversaw this work – Rosemary Ekong - r.ekong@ucl.ac.uk
Thank you!
 

Australian Government releases National Health Genomics Policy Framework

- this document was recently endorsed by state and federal health ministers to set out a vision for integrating genomics into the national health system. It was prepared after a period of consultation in which HVP members and the HVP Australian Node participated. Importantly the framework includes Data – the responsible collection, storage, use and management of genomic information - as one of five priority areas. It would be interesting to hear from members if their own national governments had produced a similar document – please let us know – Helen – hmro@unimelb.edu.au 


If you are interested, you can access the complete document here:
 
https://www.coaghealthcouncil.gov.au/Portals/0/Genomics%20Framework%20WEB_1.PDF
 
 

Topical article – Genetic Testing: what problem are we trying to solve?
By Kevin S Hughes of Harvard Medical School USA appeared in recent issue of Journal of Clinical Oncology (DOI: 10.1200/JCO.2017.74.7899) does some projections concerning demand for testing for BRCA carriers to raise some issues about identifying high risk patients and the role of population screening in prevention of hereditary cancer susceptibility cancers.
 

World Science Forum, Jordan – 7-11 November

HVP was represented at the recent World Science Forum (WSF). Members will recall that HVP has the privilege of having official relations as an NGO with UNESCO resulting from working relationship between the two organizations over the past decade.  The key theme of the meeting was focussed on how science can be used for peace. While this seems somewhat distant from HVP’s mission and activities, several issues of relevance to the work of HVP emerged:

  • The need for strong voices to support open and transparent data sharing was raised several times during the meeting; this open sharing of all kinds of data, including genomic information and bio-data; it is seen as the best means of countering misuse of information; open transparent data sharing is seen as being empowering particularly to smaller groups
  • Need to be actively involved to trans-generational exchange of knowledge and expertise – the importance of involving younger people in debates on genetics and genomics; the challenge for HVP members is how to draw more younger scientists into their work and how to attract younger people into a career involving human genetics and genomics as the demand for these skills will grow in the coming years.
 

Full Meeting Report
 

GG2020

GG2020 Challenge was involved in several key meetings during November.  Those seeking more information should contact the key people listed below.
  1. Thalassaemia Awareness Campaign: Towards Zero Thalassaemia - 26 October 2017 - Full meeting report
  2. Asia-Pacific Conference on Human Genetics – APCHG 2017 Bangkok, Thailand 8 -10 November 2017 – contact Prof Zilfalil Bin Alwi   zilfalil@usm.my
  3. African Society of Human Genetics – Cairo, Egypt 16-18 November 2017– contact Prof Raj Ramesar  raj.ramesar@uct.ac.za
  4. Meeting of International Thalassemia Federation – Thessaloniki, Greece – contact Carsten Lederer lederer@cing.ac.cy
 

LOVD

We are currently in the process of integrating LOVD (Leiden Open (source) Variation Database) under the HVP umbrella. The LOVD3 website has recently included our logo. Johan T Den Dunnen, leader of LOVD3, is an active member of HVP, currently working with countries who have yet to share their data. He also runs various training courses throughout the year.

 

YOKOHAMA, 13-15th March 2018


We encourage all members to attend our HVP sessions at the Human Genome Meeting.13–15 March 2018, Yokohama Japan. 

https://www.hugo-hgm.org/program/scientific
 

Posted by on in News
Consortium Update - October 2017
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GG2020 HAS FIRST PEER-REVIEWED PUBLICATION


Check the following link to read the first major article outlining HVP’s project-wide initiative GG2020 that focusses on haemoglobinopathies as an entry point into genomic medicine, particularly for low-resources settings. It also raises the important issue of insuring that results diverse populations are systematically included in variant databases.

http://rdcu.be/vEcO
 

ClinGen

 

ClinGen has launched a list of Clinical Laboratories Meeting Minimum Requirements for Data Sharing to Support Quality Assurance
https://www.clinicalgenome.org/lablist/
 
Accompanying paper attached and media stories below:
 
1.            Genome Web – July 17, 2017 - ClinGen Lists Labs Meeting Requirements for Quality Data Sharing on Genetic Variants https://www.genomeweb.com/genetic-research/clingen-lists-labs-meeting-requirements-quality-data-sharing-genetic-variants
2.    Diagnostics World – July 17, 2017
Heidi Rehm Calls For Sharing of Variant Interpretation Data
http://www.diagnosticsworldnews.com/2017/07/17/heidi-rehm-calls-sharing-variant-interpretation-data.aspx
3.    Genetics in Medicine GenePod – July 17, 2017
PodCast: Making sense of a deluge of variants: harnessing the power of community
http://www.nature.com/gim/podcast/archivetranscripts.html

Collecting genetic variant information in a single large database


A newly published paper in Genetics in Medicine from  colleagues based at Mt Sinai in Canada has reinforced the fundamental importance of collecting information about genetic variances in a single large database.  With so much important genetic information being used globally to understand the underlying genetic influences of diseases, researchers and clinicians need an accessible repository to share this information. This highlights activities related to the Canadian Node.

Click for more information…. 

http://www.sinaihealthsystem.ca/news/importance-of-large-database-of-genetic-variants-reinforced-in-a-new-study/

CTFR-France


From Human Mutation this important article addresses the role of the curator and the necessary curation processes required for clinical responses using the 2,000 variants identified in the CFTR (cystic fibrosis transmembrane regulator) and the issue of their interpretation being hampered by the lack of available data and resources, making patient care and genetic counselling very challenging. In response to this issue, INSERM  developed a patient-based database dedicated to the annotations of rare CFTR variants in the context of their cis- and trans-allelic combinations. Based on almost 30 years of experience of CFTR testing, CFTR-France currently compiles 16,819 variant records from 4,615 individuals with cystic fibrosis (CF) or CFTR-RD (related disorders), foetuses with ultrasound bowel
anomalies, newborns awaiting clinical diagnosis, and asymptomatic compound heterozygotes

For each of the 736 different variants reported in the database, patient characteristics and genetic information (other variations in cis or in trans) have been thoroughly checked by a dedicated curator.

Combining updated clinical, epidemiological, in silico, or in vitro functional data helps to the interpretation of unclassified and the reassessment of misclassified variants. The article explains the value of this comprehensive CFTR database as a tool for diagnostic laboratories gathering information on rare variants, especially in the context of genetic counselling, prenatal and preimplantation genetic diagnosis. Importantly CFTR-France is thus highly complementary to the international database CFTR2 focused so far on the most common CF-causing alleles. This harmonising between the national approach and the international one is important for many other HVP members. Any questions or comments should be directed to Mireille Claustres mireille.claustres@inserm.fr.

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Posted by on in Statements
Message from the Executive Chairman - Aug 2017

The Human Variome Project and Global Variome

 

Following the tragic death of Dick Cotton, it was decided to restructure the organisation of the Human Variome Project to better prepare it for the rapidly evolving world of Genomic Medicine. Before stepping down as Chairman of the Board, Chris Arnold steered the process whereby the existing Australian corporate entity responsible for HVP, known as HVP International, was closed down and a UK application moved the HVP into a new organisation called Global Variome.  This is a not-for-profit entity using the same structure as HVPI with an international Board comprising of myself, Garry Cutting, Mike Watson, Raj Ramesar, Johan Den Dunnen, Zilfalil Bin Alwi, Ingrid Winship and Julia Hasler.  Julia brings expertise relating to the operation of UNESCO having worked there for many years.  UNESCO has recognised Global Variome; with its new administrative base at the International Centre for Life in Newcastle and as the official body responsible for the HVP.  With considerable support from Tim Smith who spent a few months here on sabbatical and my assistant Amy McAllister, with whom many of you will now have interacted, we have opened a bank account, engaged accountants and successfully achieved charitable status for the new organisation.

The decision to adopt the new name was, in part, influenced by the emergence of the Global Alliance for Genomics and Health with which we collaborate in advancing the BRCA Challenge.  The advent of high volume whole genome sequencing around the world means that the majority of variants will be future identified in a diagnostic setting using high throughput sequencing devices.  GA4GH is a response to this new world and its aims significantly overlap those of HVP.  After a period of consultation, the GA4GH has shifted its focus to emphasise the computational and technical aspects of genomics; including the ethical dimension and the interplay of confidentiality and data security.  Rather than try to replicate what will become a well-resourced international effort, we need to see how we can complement their efforts and become a partner in the task of making genomics work for the whole world.

The emphasis of HVP on locally managed databases and the need for country nodes which interact at the international level remains highly relevant and can be the unique contribution of our organisation.  Along with our close partners in HGVS, we can also contribute the important task of making it possible for all health systems to benefit from genomic knowledge using a consistent and comprehensible language.  The efforts of Johan Den Dunnen to build and develop LOVD has been pivotal and we will seek to bring the curation of LOVD closer to Global Variome, while also promoting an educational programme to help clinicians and clinical scientists make best use of their data and share their knowledge.  In addition to our help with the new website (www.BRCAexchange.org) we will continue to develop our interaction and promote other disease focused databases, particularly the InSiGHT database built around the genes responsible for hereditary colorectal cancer.

Our involvement across Low and Middle Income Countries (LIMCs) has prompted the development of Global Globin 2020, with a focus on better care for people with the inherited haemolytic anaemias such as sickle cell disease and thalassaemia.  Exciting progress on this front, supported by Helen Robinson, will be the subject of our next post together with details of the HVP meeting alongside HUGO in Yokohama, Japan next March.

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