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.

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.

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.

In the same year that Vernon Ingram first showed us that changes to a single amino acid in a protein can cause disease or disorder in humans, Johan den Dunnen was born. Growing up in a time when scientific advances in the realm of human genetics were on rapid fire (do the names Meselson, Stahl, Lejeune, Guthrie and Nirenberg ring a bell?), he was inspired to study biology. Johan went on to complete his PhD in the Netherlands examining the evolution of eye-lens crystallin genes, before his research took him toward the area of genetic disease - specifically Duchenne muscular dystrophy.

As well as being an academic (currently a Professor of Medical Genome Technology at Leiden University Medical Centre), Johan, is part of another group within the community. The group boasts members such as Ozzy Osbourne, Elvis Presley, Larry King, and Glenn Close.

What they have in common (unfortunately we're not announcing a supergroup to rival the Traveling Wilburys) is that they have all had their genome sequenced.

Since the completion of the Human Genome Project in 2003, a developing commercial market has allowed an increasing number of individuals to have their genome sequenced. While for James Watson - joint discoverer of DNA - it came at a cost of around $1 million dollars, but by the time Steve Jobs sought information about his own genome to aid his cancer treatment, the cost had fallen to around $100,000.

Today genetics is not just for the wealthy. Today individuals can have access to their own genomic blueprint for around $1,000 USD.

If you're an academic or on your way down a related path, the term "publish or perish" needs no further explanation. For those outside the circle, the pressure to generate multiple high quality research publications in rapid succession may not seem unusual. How else will the worldwide science community know what you are working on? What other channels exist to share interesting pieces of data or breakthrough results?

The flip side of the argument often points out that focussing on publication quantity has detrimental effects on publication quality. This side of the argument is fuelled by reports highlighting careless mistakes in scientific literature, low reproducibility rates in repeat experiments and extreme cases of academic misconduct and the falsification of results. While all of this sounds like a horror story for scientists to deal with, what are the real implications of these errors outside of the lab? A recently published article in the Atlantic outlined one such example in a disconcerting scenario encountered by Heidi Rehm.

In addition to her role on the International Scientific Advisory Committee for the Human Variome Project, Heidi Rehm is also the Chief Laboratory Director at Partners' Laboratory for Molecular Medicine and Associate Professor of Pathology at Brigham & Women's Hospital and Harvard Medical School. Rehm's position sees her routinely provide reports on patient samples sent to Partners Laboratory from healthcare professionals around the country.

The particular situation described by Heidi Rehm pertains to a foetal blood test which returned a result indicating a variant in PTPN11, a gene which can signify an increased risk of Noonan syndrome. Using the tools at her disposal, Heidi Rehm scoured the scientific literature, finding a paper which classified the specific variant as pathogenic and indeed likely to cause Noonan syndrome. Naturally, the report she returned detailed this finding.

Since the particular sample in question crossed Heidi Rehm's path, further research by a separate group uncovered a high prevalence of the PTPN11 variant among particular ethnic groups who show no sign of the genetic disease, resoundingly disproving the earlier classification of the variant as pathogenic. The original paper that Rehm referenced was wrong.

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!

Recently I watched Sir John Burn’s interview with Alison – a very polite and lovely science teacher from the UK who unfortunately passed away one year after the interview was recorded.

From the interview, I learnt that Alison had been aware ever since she was a child that several women in her family had died in their thirties or forties from cancer.

Sadly, the medical profession (at the time) considered these cancers to be caused by environmental factors, not an underlying genetic cause.

So when Alison herself fell seriously ill and sought treatment, she asked for genetic tests, but was told that her recollections of cancer in her family were irrelevant to her condition and amounted to hearsay.

After Alison’s death, Sir John Burn wrote an editorial urging the medical community to reconsider at what point in diagnosis genetic tests should be ordered for patients. I wonder what impact Sir John Burn’s cautionary tale of Alison’s diagnosis and treatment has had, and reading through it recently, I’m reminded of the Australian Government’s announcements to reduce funding for pathology and other diagnostic services in 2016 .

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.