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Message from the Executive Chairman

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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The Human Variome Project and its new coordination arrangements

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:

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Statement from the Human Variome Project International Scientific Advisory Committee on the International Consortium of Human Phenotype Terminologies

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.

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:

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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.

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19 November, 2013

Office of Science Policy
National Institutes of Health
6705 Rockledge Drive, Suite 750
Bethesda, MD 20892
GDS@mail.nih.gov.au

Submission regarding the Draft NIH Genomic Data Sharing Policy

1. Background to Submission

The Human Variome Project is an international consortium of scientists and healthcare professionals who are working towards a significant reduction in the burden of genetic disease on the world’s populations. The aim of the Human Variome Project is to ensure that all information on genetic variation can be collected, curated, interpreted and shared freely and openly. This will lead to speedier, better and cheaper diagnosis and treatment of genetic disorders, and better insight into the causes, severity and effect of common disease. The Human Variome Project achieves its aims by establishing and maintaining the necessary standards, systems and infrastructure, by providing education and training to scientists, clinicians, genetic counsellors, other healthcare professionals and the general public and by assisting nations build their capacity in medical genetics and genomics. The Human Variome Project acts as an umbrella organisation and works to encourage communication and collaboration around its central vision.

The importance of the Human Variome Project was recognised in 2011 by the United Nations Educational, Scientific and Cultural Organisation in the Project’s admittance to Consultative Partner status.

Genetic tests for diagnostic, predictive and screening purposes are a routine part of clinical care in most modern healthcare systems, and as we discover more about the genetic determinants of our health, we can expect genetic testing to become more prevalent. At the same time, new technological advancements, lower costs and increased training and education will see genetic testing spread rapidly into routine clinical practice in countries with, to date, less advanced healthcare systems.

Despite major advances that have allowed the technical portion of genetic testing to become routine, the interpretation of clinical sequencing results remains a major challenge given the enormous amount of rare and unique genetic variation in the human population. Enabling patients to optimally benefit from genetic testing will require major advances in our understanding of genetic variation and its impact on health and disease. Open data sharing of patient genotypes and phenotypes is necessary to achieve these advances.

The Human Variome Project believes that all laboratories that undertake genetic testing for diagnostic, prognostic or screening purposes must share the molecular and phenotypic data generated or collected in the course of testing in an appropriate public database. Not sharing this data prevents comparative assessments of variant interpretations, reduces consensus building, decreases the quality of test interpretations, and allows for potential harm to patients. To this end, the Human Variome Project fully supports the recent American College of Medical Genetics and Genomics Position Statement on Public Disclosure of Clinically Relevant Genome Variants (http://short.variome.org/acmg-crgv-statement).

Further, the Human Variome Project calls on national governments, regulatory bodies and professional societies to facilitate the free and open sharing of this information by reducing legislative and procedural barriers. While the Human Variome Project recognises the sensitive nature of genetic information and accompanying clinical data, and is aware of the ethical, legal and social issues inherent in its collection, storage and use, the Project also recognises that this same information is fundamental to the practice of genetic and genomic medicine. A balance must be struck between protecting individual privacy and establishing a body of evidence capable of providing life-saving medical intervention to the population at large.

Introduction

The Human Variome Project Consortium believes that the free and open sharing of human genetic variation information will lead to improved health outcomes for all people worldwide. We also believe that the most efficient and effective means for sharing this information is via a network of gene/disease specific databases, as described by the Project’s Global Collection Architecture.

To ensure the fullest dissemination of variation information to the genetics community, we believe that all sequence variants reported in journal articles should not only be fully and accurately described within the articles that report them, but also deposited into the appropriate gene/disease specific databases prior to publication.

We acknowledged that some journals already share these values but the adoption and implementation of appropriate guidelines for manuscript authors is patchy, especially with respect to the submission of data to databases. The Human Variome Project Consortium strongly encourages all journal editors to enforce a strict, mandatory policy that all variants be correctly described and deposited into variant databases prior to publication. Such a policy is already enforced by Human Mutation and other journals represented in the Human Variome Project’s Journal Editors Interest Group, and appears to be working effectively.

This Statement lays out the ideal scope of such a policy. We do, however, recognise that some journals will be unable to impose all aspects of this statement.

Today is a sad day. Our colleague, collaborator, champion and friend, Professor David Rimoin, Inaugural Chair of our International Scientific Advisory Committee, passed away after a brief battle with pancreatic cancer.

David was a true friend of the Human Variome Project. Despite his many other commitments: Director of the Medical Genetics Institute and Steven Spielberg Family Chair in Pediatrics Cedars-Sinai, Professor of Pediatrics, Medicine, and Human Genetics at the David Geffen School of Medicine at the University of California, Los Angeles, David's support and work for the Human Variome Project was tireless. David's tenure as the first Chair of the Project's International Scientific Advisory Committee was incredibly productive. In this role he oversaw the establishment and growth of the Human Variome Project Consortium to include over 700 individual members, twelve HVP Country Nodes and 33 gene/disease specific databases. David was also particularly instrumental in starting discussions around establishing an HVP Country Node in the United States.

David will be sorely missed by every member of the Human Variome Project Consortium. His energy and enthusiasm for the Project, and for the field of medical genetics, was evident to all who were lucky enough to meet him. At our meetings, he was always a leading voice in every discussion. He will be missed, and our upcoming 4th biennial meeting in Paris in just a few short weeks, will not be the same without him.

Our thoughts are with David's family at this time.

The international Human Variome Project Consortium and the Human Variome Project Chinese Node

Recognising that our genes are fundamental to human life and diversity and are a common thread that binds all peoples and cultures,

Emphasising that the free and open sharing of information on genetic variations and their effects will improve human health by enabling faster, cheaper and more accurate diagnosis, therapy and treatment,

Recalling that Article 1 of the UNESCO Universal Declaration on the Human Genome and Human Rights states, “The human genome underlies the fundamental unity of all members of the human family, as well as the recognition of their inherent dignity and diversity,”

Noting that the mantra of the Human Variome Project is sharing data · reducing disease, and

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