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DRAFT paper for comment of Members - Minimal Content Requirement for Genomic Variant Databases

 

Minimal Content Requirement for Genomic Variant Databases –

DRAFT paper for comment of Members

Click here to view the paper

 

Members are invited to review and comment on this important paper. It will form the basis of clear guidance to Variant database administrators, database curators as well as submitters and users. We all know that improving the utility of variant databases is a continuous process. To date, databases have been developed in the absence of practical guidance which has created  a lot of inconsistencies. HVP members have thought that it is timely to provide some clear guidance and practical tools to create greater consistency across the globe.

This paper is the result of the work of many HVP members and we thank them very much – in particular the two co-authors – Peter Taschner and Martina Witsch-Baumgartner  



Deadline for comments – Monday 17 December 2018 – comments to Helen Robinson – hmro@unimelb.edu.au

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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

 

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
 

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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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