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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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DRAFT proposal for comment from members: SVD-WG008 (RefSeq)
 

We would appreciate your input... 



Proposal SVD-WG008 (RefSeq) 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 - Monday 30th September - comments to varnomen@variome.org or amy@variome.org

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

 

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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

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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

 

 
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                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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HGVS nomenclature course @ ESHG 2018

 

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                Milan, Friday June 15, 2018

with the kind support of the European Society of Human Genetics

 

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