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Dear colleagues and friends,

It has been sometime since I posted an update.

The Human Variome Project

The Human Variome Project is a global consortium with 1300+ members across 81 countries, that is committed to building capacity worldwide in the collection, curation, interpretation and open sharing of information on variation in the human genome. It has both Associate NGO status with UNESCO, and a Memorandum of understanding with the World Health Organisation.

For 10 years, the HVP has been coordinated by an Australian body, Human Variome Project International Ltd, a not-for-profit, Australian public company limited by guarantee.

In the last few years:

Catching a wave is one thing, but imagine riding a single wave for over 17 kilometres. This is exactly what a team of Australian surfers have done, all in the name of a very important cause. James Cotton, Roger Gamble and Zig Van Sluys set out upon the Kampar River in Indonesia's Riau Province where the 'bono' tidal wave carried them to a world record for the longest wave surfed as a team - with a total of 37 kilometres tallied between the three. James Cotton, son of the late Dick Cotton - Human Variome Project founder, clocked up an incredible 17.2 km stretch, setting the individual world record of the longest wave surfed. The wave - which at certain points can reach to 3 meters high - must be seen to be believed, so we've included some photos to help paint the picture!

In addition to this remarkable effort, the three set themselves the ambitious task of raising $50,000 for the Human Variome Project, a cause close to their hearts, to help ensure that all information on genetic variation and its effect on human health can be collected, curated, interpreted and shared freely and openly. With the latest count at over $47,600 it is clear that nothing stands in the way of these determined individuals. The International Coordinating Office sends our heartiest congratulations and deepest thanks to the Team at World Record Surfing for a Cause - James, Roger and Zig - as well as all the sponsors, donators and supporters for their contribution to raising awareness and funds for the Human Variome Project.

Last week The Human Variome Project and the Open Knowledge Foundation, hosted a meetup at ThoughtWorks on Collins St in Melbourne. Professor Dr. Johan den Dunnen shook things up with his idea for a ‘DNA-bank’ - a place where account holders have full discretion over access to their genetic sequence for research or medical purposes.

Johan made an unfamiliar topic easily relatable with his presentation featuring both comedic and personal details – we even got to see Johan’s own genome! Visualised into a starfield type array of variants, each with different colours like Christmas baubles. Red signalled a variant that caused a protein to stop working – Johan had a few reds – which made us all think we have reds too, but few of us would know if we did – as at this stage, knowing your own genome is limited to only a few social circles like medical genomicists, early adopters in the direct-to-consumer market and the few people who’ve had genetic tests through primary healthcare.

There’s another joint meetup coming up on at 6pm on March 9th at ThoughtWorks featuring Professor Ingrid Winship. We are really lucky to have Professor Winship speaking – as the Chair of Adult Clinical Genetics at the University of Melbourne and the Executive Director of Research for Melbourne Health (among other important positions), Professor Winship is a very knowledgeable (and busy!) leader in Australia’s healthcare scene.

Visit http://www.meetup.com/Open-Knowledge-Melbourne/events/228798812/ for more information and to register for the free event.

Hope to see you there!

The Committee congratulates the representatives of the nine phenotype terminologies represented on the International Consortium of Human Phenotype Terminologies (ICHPT; http://www.irdirc.org/ichpt/) on the recent release of a core set of 2,086 terms that represent the major phenotypic abnormalities encountered in persons with rare diseases.

The Committee notes that the Human Variome Project exists to build capacity in the practice of responsible genomics and focusses on increasing both the quality and quantity of genomic knowledge that is collected, curated, interpreted and shared for clinical practice, and that the use of a common language to unambiguously refer to concepts is vital to this effort. Such common languages are already in place for some aspects of the work relevant to the Human Variome Project—the Committee especially notes the HGVS Nomenclature for the description of sequence variants—and now, with the release of this work by the International Consortium of Human Phenotype Terminologies, the beginnings of a similar language are in place for phenotypic features.

The ICHPT core terms provide both terms and definitions for the most common phenotypic features represented in the ICHPT member terminologies as well as cross references to a number of existing terminologies, including the Human Phenotype Ontology, which has become the de-facto standard for representing human phenotypes. This provides researchers that require resources offered by only one of the terminologies that have agreed on the core set with the ability to use their preferred terminology but still be able to integrate their data at a certain level of granularity by subsuming annotations to the level of the common terms.

The Committee believes that widespread adoption of this set of terms will allow easier exchange and integration of data from specialist and generalist databases, sophisticated search algorithms for biomedical literature, and the comprehensive and accurate documentation of phenotypic abnormalities, especially in hospital information systems. We therefore make the following recommendations:

1. Phenotypic features should be represented in all genetic variation databases using terms from a terminology that has agreed to and defined cross-references to the ICHPT core set of phenotypic feature terms; and
2. Existing phenotype terminologies that have not yet agreed to the ICHPT core set of terms and defined cross-references between their terms and the ICHPT core set should do so at the earliest possible opportunity.

The Human Variome Project is pleased to announce the newest appointed members of the International Scientific Advisory Committee, Jordan Lerner-Ellis and Juergen Reichardt.

Jordan Lerner-Ellis is currently Head of Advanced Molecular Diagnostics at Toronto’s Mount Sinai Hospital. He holds the position of Assistant Professor in the University of Toronto’s Department of Laboratory Medicine and Pathobiology and is an Associate at the Ontario Institute for Cancer Research.

Juergen Reichardt is currently the Head of School, Pharmacy and Molecular Sciences at James Cook University. Furthermore, he serves as the Associate Dean Research in the Faculty of Medicine, Health and Molecular Sciences at James Cook University.

We are thrilled to welcome our new additions to the team and look forward to the advances that will stem from their contribution.

The Board of Human Variome Project International Limited is pleased to announce the appointment of two new directors to the Board. We welcome James Angus and Zhonghua Gao to the team.

Zhonghua Gao heads the Beijing China Health Huayang Institute of Gene Technology and is the newly appointed Director of the HVP China Node Working Committee. 

James Angus is a Professor in the Department of Pharmacology and Therapeutics at the University of Melbourne and is the former Dean of the University of Melbourne Faculty of Medicine, Dentistry and Health Sciences.

Both Zhonghua and James bring a depth of experience and new perspectives to the Board. 

We are also pleased to welcome Kathryn North as an adviser to the Board on strategy and activities, and as formal liaison between the Human Variome Project and the Global Alliance for Genomics and Health Steering Committee. Kathryn is currently the Director of the Murdoch Childrens Research Institute in Melbourne, Australia and the David Danks Professor of Child Health Research at the University of Melbourne.

It is with profound sadness that I advise that Professor Richard Cotton passed away peacefully in his sleep on Sunday morning.

We here at the International Coordinating Office, as I'm sure are you, are deeply saddened and shocked by this tragic news.

Dick provided us with leadership that inspired us all to embrace his global vision. He leaves behind a truly remarkable legacy. His vision in the field of the collection and sharing of human genetic variants is legendary. He was one of the first to realize that DNA sequencing would change the world and that genetic diagnostics would be based on sharing information on genes, variants and phenotypes. Without sharing this data, diagnosis would not be possible and optimal care to the patients and their family's non-existent.

He spent the last 30 years of his life persuading people to share his vision and what they know about genes, variants and phenotypes. He started the journal Human Mutation, initiated the alternating bi-annual International Mutation Detection Workshops and HUGO Mutation Detection Courses, the HUGO Mutation Database initiative, stood at the basis of the HGVS recommendations to describe DNA variants and organizations like the Human Genome Variation Society (HGVS) and since 2006, the Human Variome Project (HVP). Irrespective of whether all these efforts were as successful as he might have wished, Dick Cotton was the enthusiastic driver that mobilized many volunteers, to spread the word, do some work and make a difference.

From the start he realized the importance of developing a common, world-wide accepted language to describe DNA variants. He gave a kick-start to suggested standards like this by offering the option to publish them in the journal Human Mutation. When standards matured he dared to take the risk by demanding their use before accepting papers for publication in Human Mutation.

Media Release
For Immediate Release

Kuala Lumpur, 17 March 2015—Patients with one of a number of devastating genetic blood disorders, such as thalassemia and sickle cell anaemia, will benefit significantly in the coming years from a new international project announced today at the annual Human Genome Organisation meeting in Kuala Lumpur. The Global Globin 2020 Challenge (GG2020), an initiative of the Human Variome Project—an international scientific NGO working with UNESCO and WHO to build medical genetics and genomics capacity, particularly in low- and middle-income countries—will apply recent developments in human genomics involving the systematic collection and sharing of genetic variation data to fighting these blood disorders, referred to technically as haemolytic anaemias.

In particular, the Challenge will build an evidence base for the better management of delivery of local treatment, care and eventually cure for these diseases by ensuring that there is sufficient local capacity to deliver services. It is believed that the Challenge will put in place the skills and expertise in genomic medicine needed to effectively tackle other health issues in these countries as well.
The Challenge is being led by two leading geneticists, Professor Zilfalil bin Alwi from Malaysia and Professor Raj Ramesar from South Africa. Both are members of the Human Variome Project Board and can see the benefits this project will bring to their patients and others in South East Asia, Africa and the rest of the world.

Human Variome Project International (HVPI) Chairman, Chris Arnold, who chaired the HUGO session introducing the project, thanked the GG2020 challenge co–chairs and fellow HVPI directors, Professor Zilfalil Bin Alwi, from Universitie Sains Malaysia and Professor Raj Ramesar from the University of Cape Town South Africa for their leadership and willingness to coordinate this major global initiative. Mr Arnold stated “The haemolytic anaemias collectively, are cause for significant morbidity and mortality, especially in parts of the world where health systems are often less well developed. Children are often most severely affected. Despite much being known for a long time about the genetics and biology of the haemolytic anaemias and this knowledge being used successfully in some countries to systematically reduce burden of disease, low- and middle-income countries have remained practically untouched by this knowledge and innovations.”

In launching the Challenge, Professor bin Alwi said, “The Malaysian Node of Human Variome Project is honoured to be given the privilege to co-chair this Global Globin Initiative. Hemoglobinopathy, in particular Thalassaemia, is a common disease in Malaysia where about 5% of the population are carriers of the disease".

In August, the National Health and Medical Research Council in Australia called for comment on a draft of their "Draft Principles for the translation of ‘omics’-based tests from discovery to health care". The Human Variome Project International Scientific Committee submitted the following response.

Dear Professor Ward,

On behalf of the Human Variome Project International Scientific Advisory Committee, we congratulate you on the work of the National Health and Medical Research Council (NHMRC) Human Genetics Advisory Committee and the NHMRC Secretariat in producing the Principles for the translation of ‘omics’-based tests from discovery to health care and we welcome the opportunity to respond as part of the document’s public consultation. These are complex issues that many health systems and research funding bodies around the world are grappling with. We are pleased to have been invited by the NHMRC Secretariat to share the expertise of our members and provide an international perspective to these principles.

As you are well aware, the Human Variome Project is an international non-governmental organisation that is working to ensure that all information on genetic variation and its effect on human health can be collected, curated, interpreted and shared freely and openly.

The Human Variome Project provides a central coordinating function for national and international efforts to integrate the collection, curation, interpretation and sharing of information on variation in the human genome into routine clinical practice and research. We are an active and growing Consortium of over 1,100 individual researchers, healthcare professionals and policy makers and organisations from 81 countries that collaborate to develop and maintain the necessary standards, systems and infrastructure to support global scale genomic knowledge sharing. The Project itself is not directly involved in the development and operation of physical data storage and sharing infrastructure; that is the responsibility of international disease groups, national consortiums/health systems and individual members. Rather, the Project exists to assist these groups by:

In August, the Global Alliance for Genomics and Health called for comment on their draft constitution. As a founding member of the Global Alliance, the Human Variome Project issued the following response.

Dear Professor Altshuler,

Human Variome Project International Limited (HVPI) welcomes the development of a draft Global Alliance for Genomics and Health (GA4GH) constitution for comment by participating organisations. Constitutions are important documents that lay the foundation for almost every part of an organisation’s existence and it bodes well that GA4GH has taken the laudable step of engaging in genuine consultation with its member organisations on this document. To further promote dialogue and discussion, we might suggest that the feedback that is received on this document be placed on a section of the GA4GH website, either publicly accessible or restricted to GA4GH member organisations.

We believe that the document, as it currently stands, is a good first step towards defining a constitution for the GA4GH. We are pleased to see that important concepts and principles such as collaboration, ethics, responsible data sharing, transparency and openness feature heavily in the document. We look forward to participating in the process of articulating the detail necessary to implement these concepts.

We recognise that there are areas that will require further consideration over time, some of which we will refer to in this response.