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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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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

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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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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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Consortium Update - August 2017

 

 
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HVP and IRDiRC


Human Variome Project (HVP) and IRDiRC decided to join forces on the topic of Recommended Systems. As a consequence a series of HVP Recommended Systems (http://www.humanvariomeproject.org/solutions/recommended-systems.html) are now also recognised as IRDiRC Recognized Resources (http://www.irdirc.org/activities/irdirc-recognized-resources/), systems dated May 17).
 

LOVD3

Which countries actively share data on genes, variants and phenotypes?


The LOVD database recently released a new service. Interested in what your country shares?  Try the international country code in front of ".LOVD.org" and check, e.g. nl.LOVD.org for Netherlands and au.LOVD.orgfor Australia. Then check "Variants in Individuals from xx", i.e. variants linked to an individual from a specific country. Or "Variants by Submitters from xx", i.e. data submitted by somebody from a specific country. The data retrieved are from the LOVD3 shared database. Is your country already sharing?  If not, want to make a change? What's stopping you? Register and start, it's that simple!
 

Meeting Report: The 14th International Symposium on Variants in the Genome
NH Collection Santiago de Compostela
June 5 - 7 2017


The 14th International Symposium on Variants in the Genome took place in Santiago de Compostela, a UNESCO world heritage city, from 5-8 June 2017, with participation of 170 delegates from 32 countries. The meeting addressed recent advances on the genome and genetic variation, such as genome structure and function, country-wide genome projects, transcript and splicing analysis, novel sequencing methods, informatics pipelines, and data sharing networks.  Research, as well as diagnostic applications were discussed in depth. Special sessions were dedicated to pharmacogenomics and drug discovery – with presentation of the Innopharma drug-screening platform – and to the BRCA Challenge, chaired by Prof. Sir John Burn. Distinguished invited speakers included P Donnelly (meiosis), J Dopazo (computational tools), I Gut (genome sequencing), P Robinson (phenotype ontologies), J Surrallés (Fanconi anemia), G Ratsch (BRCA exchange), S Aradhya (Claire Turnbull (Genomics England), W Parson and C Phillips (forensic genetics). Two workshops were focused, respectively, on variant nomenclature and clinical interpretation. Commercially-sponsored presentations and workshops also provided opportunities to discuss practical questions. Over 30 studies were presented as poster or platform communications. We thank all our sponsors for helping to make this event possible and look forward to the next meeting in 2019.

Meeting Report: 2017 InSIGHT Biennial Meeting
Florence, Italy
5th - 8th July 2017 


In a session co-chaired by ISAC member, Marc Greenblatt entitled Human Genome Variation and the role of InSiGHT,  a range HVP activities were  presented at the recent InSiGHT meeting in Florence:
Sir John Burn, Chair of HVP’s Board outlined the progress of HVP’s collaborative project undertaken with GA4HG – the BRCA Challenge; this initiative involves many HVP members and was presented as an example of how collaborative networks of multidisciplinary professionals are currently working to harmonise their efforts in database curation and clinical interpretation; This project has many goals that mirror those of InSiGHT and much may be gained by exchanging lessons learned.

Zilfalil Bin Alwi, HVP Board member presented HVP’s project-wide initiative the Global Globin 2020 Challenge which aims to promote skills and knowledge required for biomolecular diagnostics,  variant curation and interpretation in low and middle income countries; haemoglobinopathies are the focus for this project because in many parts of the world, the application of genomic knowledge has not been leveraged effectively for better health care delivery utilising simple diagnosis to determine carrier status.
Helen Robinson from HVP’s office gave a presentation on the work of HVP Country Nodes and how they could be used to broaden and deepen the work of InSiGHT through linking up with networks operating in many different regions of the world; increasingly HVP Country Nodes are becoming effective entry points for gaining access the genomic expertise in a country.
Lastly, Jon Paul Plazzer, curator of the InSiGHT international variant database presented the new version of their database using  LOVD3; this database is a model for other international variant databases; it has an active interpretation committee and receives several thousand visits every month thus demonstrating how the overall goals of HVP can be realised in a very concrete manner.

 

Meeting Report: Global Globin 2020 Challenge (GG2020) Conference 

Moving Towards Zero Thalassaemia
Kuala Lumpur
17-18 July 2017


On 16th July 2017, the Global Globin 2020 Challenge (GG2020) annual meeting was held at the Impiana KLCC Hotel, Kuala Lumpur. The meeting was attended by fourteen GG2020 members from nine countries. Several issues were discussed during the meeting, including the development of the GG2020 Thalassaemia Kit. On the following day, the inaugural conference on GG2020, with the theme of “Moving Towards Zero Thalassaemia”, was held at the same venue. The conference was attended by a total of 108 participants, which included 23 international delegates from 10 countries comprising of 10 invited speakers. The opening ceremony on the 17thJuly 2017 began with welcoming remarks by the chairman of GG2020 Conference, Professor Zilfalil Alwi, followed by the chairman of the board of directors of Human Variome Project (HVP), Professor Sir John Burn and the Dean of School of Medical Sciences, Universiti Sains Malaysia, Professor Dr. Shaiful Bahari Ismail. The event was officiated by the deputy minister of Higher Education, Datuk Dr. Mary Yap Kain Ching. This was followed by a performance from MyThal Club Universiti Kebangsaan Malaysia Medical Centre (UKMMC), a club involving thalassaemia patients, their families and medical practitioners. The deputy minister of Higher Education then witnessed the exchange ceremony of Memorandum of Understanding between Universiti Sains Malaysia and Global Variome. Fifteen speakers from nine countries (Malaysia, Indonesia, Singapore, Thailand, India, Italy, Cyprus, Egypt and Pakistan) participated in this conference and shared their knowledge and experience on thalassaemia during the symposia. In general, the symposia covered topics ranging from the epidemiology of thalassaemia and cutting-edge topics such as stem cell therapy. A total of 42 ePosters were presented at the conference and three best posters were selected as the winners of the poster competition. Following the success of this inaugural conference, GG2020 hopes to make it as an annual event and see it becoming more successful in the future.  
 

Upcoming Meetings


ASHG – 17–21 October 2017, Orlando USA
HVP: 2nd Variant Effect Prediction Training Course – 6–8 November 2017, Prague
A-PCHG – 8–10 November 2017, Bangkok Thailand
African Society of Human Genetics – 7-10 November Cairo, Egypt
World Science Forum – 7–10 November Amman Jordan
TIF – 17-19 November - Thessaloniki, Greece.
HUGO & HVP meeting 13–15 March 2018, Yokohama Japan 

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Consortium Update - May 2017
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Including diverse populations in genomics

For those attending ESHG this year, or those interested in health genomics in communities with diverse populations HVP will be participating in the

following workshop.  The workshop will profile the work of HVP Country Nodes and what we have learned so far from the work of the Global Globin

2020 Challenge.  The presentations hope to spark discussion with a particular emphasis on what the global community of geneticists can do to

tackle these issues in a meaningful way over the next five years.

 

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