Month: March 2018

Over 500 researchers granted access to the Genomics England Research Environment

• Over 500 researchers have been granted access to the Genomics England Research Environment, enabling them to carry out pioneering research on the 100,000 Genomes Project dataset.

• Genomics England has also adopted the bioinformatics platform Galaxy, providing initial access to students on the MSc in Genomic Medicine course with thousands of genomic analysis tools.

The Genomics England Clinical Interpretation Partnership (GeCIP) is an international consortium of researchers, clinicians and trainees, established to improve understanding and practice of clinical genomics, and uncover new medical insights for patients. Over 2,700 people have come together into 42 research groups, known as ‘domains’. These GeCIP domains are either disease-focused or cross-cutting.

In June 2017 we gave access to our Research Environment, which contains de-identified data from the 100,000 Genomes Project, to a small group of GeCIP members. These members were provided with a subset of data and tasked with testing the environment’s usability and its analysis tools.

Today, we’re excited to announce that over 500 GeCIP researchers, from UK and international institutions, have been granted access to the Genomics England Research Environment. The researchers are part of these 11 GeCIP domains:

Cancer Rare Disease Cross-cutting
Colorectal cancer Neurology Quantitative methods, machine learning and functional genomics
Breast cancer Endocrine and metabolism
Lung cancer Hearing and sight
Ovarian cancer Inherited cancer predisposition
Prostate cancer Renal

These researchers will be able to work on the data in line with the codes of conduct set out in the GeCIP Rules, Publication Policy, publication moratorium, and their approved research proposals. Over the next few months, more GeCIP domains will be granted access to the Research Environment.

Research Environment file structure

One of the new tools we’ve embedded within the Research Environment is the well-known bioinformatics platform, Galaxy. The open-source platform contains over 5,000 tools that enable researchers to run multiple analyses on genomic data (called ‘workflows’) and visualise their results.

Galaxy is currently available to students on the MSc in Genomic Medicine course.

Prof. Mark Caulfield, Chief Scientist at Genomics England said:

The 100,000 Genomes Project now has the largest number of whole genomes with associated clinical data anywhere in the world. With the first set of GeCIP researchers being granted access to this de-identified data, we’re enabling the translation genomic research into direct patient care for years to come.


Human genome pioneer Professor Sir John Sulston dies

Professor Sir John Sulston. Image Credit: Wellcome

The Wellcome Sanger Institute has announced today the death of their founding director and pioneering scientist, Professor Sir John Sulston.

Sir John founded and directed the Sanger Institute, then Sanger Centre, from 1992 to 2000, leading a historic period of genetic discovery. He led the UK’s contribution to the draft Human Genome, a monumental effort that laid the foundations for the research that is transforming healthcare and understanding of disease today.

Professor Mark Caulfield, Chief Scientist at Genomics England said:

John Sulston was an outstanding scientist who created the Sanger Institute. John’s work and leadership in the Human Genome Project has led to major transformations in research and medicine. The 100,000 Genomes Project is one global endeavour that would not be here without his original contribution.

Professor Tim Hubbard, who worked with Sir John on the Human Genome Project, and who is now Head of Genome Analysis at Genomics England said:

John was an inspirational scientist, mentor and friend. Highly principled, he argued for the reference human genome sequence to be freely available to all, to maximise its benefit for humanity. Today’s requirements for scientific data and results to be shared openly have built on that example. The incredible progress in genomics over the last 15 years are a testament to the benefits of this openness.

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Celebrating International Women’s Day – a blog from Joanne Hackett

As part of the BioIndustry Association’s celebration of International Women’s Day today, Genomics England’s chief commercial officer Professor Joanne Hackett will be joining Dr Jelena Aleksic, founder and chief executive of GeneAdviser, at a networking evening to explore the topic of genomics and data protection.

BIA’s Women in Biotech Networking Evenings were created for attendees to connect with women from across the sector, share success stories and hear from inspirational speakers. Each event explores a different theme, reflecting speakers’ personal career paths as successful innovators in life sciences. As an academic, entrepreneur, investor and yoga instructor, Joanne is delighted to be taking part. Here she explains why. Namaste genomes!

Joanne Hackett

“Genomic medicine has been a major part of my life, both professionally and personally. I have Coeliac Disease which was only diagnosed by sequencing. It may sound dramatic but genomic medicine has saved my life.

As chief commercial officer at Genomics England, I am revolutionising healthcare in the UK.  We have the world’s largest number of whole genomes with associated clinical data which is already transforming patient’s lives as well as the wider healthcare system. We’re already beginning to make a mainstream genomics medicine service a reality in the UK. This year, whole genome sequencing becomes part of routine clinical care. This is the first time this has happened anywhere in the world. I find this absolutely amazing.

Today I would like to celebrate two things – the success of International Women’s Day, and what’s  happening in the UK’s genomics industry; the huge potential and opportunity that’s there. Realising this potential fully demands more as this transformation can only take place with really solid and productive academic and industry partnerships.

My passion is creating collaborations and relentlessly pursuing better health for all – and this is what I do every day. It is now my duty to pay it forward. This is why I mentor and support individuals on the NHS Clinical Entrepreneur Training Programme, NHS Innovation Accelerator, and DigitalHealth.London Accelerator. I think that the time for talking about genomic potential is past. It’s time to talk to business − and forge partnerships on an industrial scale.”

The networking event takes place this evening in London, hosted by Instinctif Partners.

Joanne has been actively involved in clinical research for over 20 years in North America, Europe and the UK. An accomplished entrepreneur, scientist and strategist, she has experience in the execution and management of complex business transactions, as well as broad business development experience in negotiation, execution and management of hundreds of transactions with pharma, biotech, academia and non-profit organisations.

Genomics England appoints global genomics champion as first CEO

Professor John Mattick

Genomics England announces the appointment of its first Chief Executive Officer (CEO) today. Global genomics pioneer Professor John Mattick will join Genomics England in June. He will lead the organisation as work done in the 100,000 Genomes Project provides the foundation for the systems NHS England is mobilising in its ground breaking Genomic Medicine Service.

Sir John Chisholm, Executive Chairman since the foundation of Genomics England in 2013, will hand over executive responsibility to Professor Mattick. Key objectives will be to shape and drive the strategy needed to realise the potential of genomics in the UK, work in partnership with the NHS, build relationships with patients and the public, further genomic discovery, and work with stakeholders across government, academia and industry to deliver lasting value for patients, the public and the economy.

Professor Mattick comes to Genomics England from the Australia-based and globally respected Garvan Institute of Medical Research, which he has led since 2012. Under his stewardship, the Garvan has embedded genomics, bioinformatics and big data at the centre of its research programmes – making the Garvan one of the leading exponents of whole genome sequencing in the world.

Sir John Chisholm said:

“In a very high calibre field, Professor Mattick emerged as the stand-out candidate. He has pioneered whole genome sequencing and overseen the Garvan Institute’s transformation into one of the most respected genomics centres in the world. We were clear from the outset that we would seek the best candidate – irrespective of nationality − to ensure the success of genomic medicine in this country. Professor Mattick is that candidate.”

Throughout his distinguished career, Professor Mattick has championed genome research and the development of national research facilities, for which he was awarded the Order of Australia and the Australian Government Centenary Medal. He has received international recognition for his scientific contributions to understanding the human genome, specifically his work showing that most of the genome is not evolutionary ‘junk’ as previously thought, but rather is devoted to an extensive RNA regulatory system that organises human development.

Most recently he has been awarded the 2011 International Union of Biochemistry and Molecular Biology (IUBMB) Medal, the 2012 Human Genome Organization Chen Award for Distinguished Achievement in Genetic and Genomic Research, and the 2014 University of Texas MD Anderson Cancer Center Bertner Memorial Award for Distinguished Contributions to Cancer Research.

Professor Mattick will continue his academic career while in the UK at the University Of Oxford’s Green Templeton College. He has been elected to a Senior Research Fellowship at the College for one day a week, which will allow him to continue his pioneering genomics work and strengthen links with the UK research community.

Professor John Mattick said:

“Genomics England is leading the world in bringing genomics into the clinic, understanding the genetic components of disease and translating this knowledge into mainstream healthcare. Bringing genomics to the people will revolutionise medical research, vastly improve personal health and transform the quality and efficiency of the healthcare system, not just in the UK but around the world.

“I am honoured to be asked to lead the organisation at such an exciting and important time. I have spent my professional life exploring the human genome and promoting its importance to understanding human biology, which I regard as the great quest of our age. It very much feels like my career to date has been preparing me for this role and it is an opportunity I intend to fully realise − for the benefit of patients, society and the UK economy.”

Reacting to the announcement, Parliamentary Under Secretary of State at the Department of Health and Social Care, Lord O’Shaughnessy, said:

“I am delighted to welcome Professor John Mattick as the new CEO of Genomics England. As a pioneering individual in his field, he will bring a wealth of knowledge to the role and help us to strengthen the UK’s position as world leader in genome medicine.”

Ethics and Social Science  – a community in partnership

Last month the Ethics and Social Science Genomics England Clinical Interpretation Partnership (GeCIP) held its first national community meeting in London. Alev Sen, an ESRC-funded PhD Fellow at Genomics England, describes some of the day’s highlights.

It’s not that often that over 100 leading ethics and social science researchers in the field of genomics come together with patients and families, clinicians, scientists, and policy-makers from across the UK to look at how we can contribute to world-class research and inform the future of genomics.  It was a lively and informative day, with many more engaging online via social media.

The future of genomics

Chief Medical Officer Professor Dame Sally Davies began her opening keynote by considering the progress that had been made on realising the ‘genomic dream’ of making genomics available to more NHS patients – something she had first outlined in her 2016 annual report Generation Genome. She described the setting up of the National Genomics Board by the Secretary of State for Health to support this vision, NHS England’s programme in partnership with Genomics England to develop a National Genomic Medicine Service, the recent Life Sciences Sector Deal between government and the life sciences industry, and the current review for the renewal of the Concordat and Moratorium on Genetics and Insurance between the government and the Association of British Insurers (ABI).

Dame Sally discussed ethical and societal considerations as key to the future of genomics in UK healthcare, highlighting the dedicated chapters in Generation Genome on the social contact for genomics in the NHS and genetic information and insurance. She finished by urging us to build on  learning from the 100 000 Genomes Project and the NHS Genomic Medicine Centres (GMCs) as a basis for internationally recognised and respected ethical approaches.

Research in the 100,000 Genomes Project

Genomics England’s Chief Scientist Professor Mark Caulfield followed with an update on the 100,000 Genomes Project. He gave a preview of the Genomics England Research Environment – the IT research platform housing genomes and clinical data from the project. In between recently reaching the 50,000 whole human genome sequences landmark, Mark highlighted cases of participants receiving diagnosis and treatment options as a result of taking part in the project.

Mark discussed opportunities for research through the GeCIP structure, including scope for partnership working between world-leading researchers, clinical academics and industry, and controlled access to genomic and clinical data and patients and family participants following review and approval.

GeCIP conversations

Possibilities for the Ethics and Social Science GeCIP were explored in a series of conversations with key research partners and stakeholders held by members of the GeCIP and chaired by Professor Michael Parker.

Talking to Dr Pauline McCormack, Ms Hannah Podd and Ms Shelley Simmonds, participants in the 100,000 Genomes Project, gave personal and frank accounts which were both insightful and illuminating.

Dr Saskia Sanderson talked with the Wellcome Sanger Institute’s Dr Matthew Hurles about interdisciplinary approaches to translating genomics into patient benefits.

Finally, Professor Richard Ashcroft and Mr Hugh Whittall, Director of the Nuffield Council on Bioethics, discussed bringing academic experience and evidence to bear on policy problems for genomic medicine and science.

These discussions led on to presentations on research already underway in the Ethics and Social Science GeCIP.

  • In their keynote, Professor Anneke Lucassen and Professor Bobbie Farsides presented their new research on ethical preparedness in genomic medicine (the EPPiGEN project) supported by a Wellcome Trust Collaborative award. Anneke and Bobbie discussed the need for their research in the context of genomic medicine presenting new and challenging interactions for healthcare professionals and patients and planned roll out across the NHS. They had built on learning and collaboration in the Ethics and Social Science GeCIP, from a national forum for professionals involved in the delivery of the 100 000 Genomes Project and from ethics research in NHS GMCs, as part of the journey to developing their study.
  • Dr Felicity Boardman described the social and ethical implications of pre-conception genetic screening for conditions of uncertain or variable prognosis
  • Ms Mavis Machirori presented work on the implications for future genomic services of BME women’s decision-making for risk reduction after BRCA testing
  • Dr Celine Lewis described young people’s experience of taking part in the 100,000 Genomes Project, and
  • Dr Ingrid Slade discussed clinical genomic medicine and the need for a public health ethics account.

Opportunities for the future

The day’s final discussion explored the question of ‘what next’ for the Ethics and Social Science GeCIP. The panel discussed the scope for research using diverse methodologies from large-scale cohort studies to in-depth scholarly work; informing the decisions of policy-makers, in particular through research on the experiences and views of patients, publics and practitioners; and developing fit-for-purpose patient and public involvement approaches as genomics moves further into the NHS. The panel agreed that there were wide-ranging possibilities for future research facilitated through the GeCIP with potential to contribute academic value and make a difference to the future of genomic medicine and science.

This first national meeting of the Ethics and Social Science GeCIP was brought to a close by Professor Michael Parker expressing the need to build on engagement and momentum from the event. He called for continued ambition for research on the ethical aspects and social implications of genomics, highlighting the scale of transformation for UK healthcare.

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