Category: Genomics England

Response to Science and Technology Committee Report on Genomics and Genome Editing in the NHS

The House of Commons Science and Technology Committee has today (20 April) published its report on Genomics and Genome Editing in the NHS.

In response, Sir John Chisholm said:

“I welcome the House of Commons Science and Technology Committee Report on Genomics and Genome Editing, published today. The report is a thorough and thoughtful exploration of the tremendous opportunities that genomics offers to the UK – its people, its health service and its economy.

“The Committee also recognises the huge strides that we have made – placing the UK at the leading edge of genomics discovery. As the report stresses, now is the time for the UK to overcome remaining challenges and capitalise on its global leadership − delivering genomic medicine in the NHS, improving patient outcomes and realising economic opportunities across the world.”

Genomics England uses MongoDB to power the data science behind the 100,000 Genomes Project

Genomics England is using data platform MongoDB to power the data science that makes the 100,000 Genomes Project possible. Our partnership with MongoDB allows the processing time for complex queries to be reduced from hours to milliseconds, which means scientists can discover new insights more quickly.

Genomics England, working with the NHS, is sequencing 100,000 genomes from patients with rare diseases and their families, as well as patients with common cancer. On average, 1,000 genomes are sequenced per week, which amounts to around 10 terabytes of data per day. To manage this immense and sensitive data set, Genomics England uses MongoDB Enterprise Advanced.

Augusto Rendon, Director of Bioinformatics at Genomics England, said:

Managing clinical and genomic data at this scale and complexity has presented interesting challenges. That’s why adopting MongoDB has been vital to getting the 100,000 Genomes Project off the ground. It has provided us with great flexibility to store and analyse these complex data sets together. This will ultimately help us to realise the benefits of the Project – delivering better diagnostic approaches for patients and new discoveries for the research community.

MongoDB Enterprise Advanced satisfied these requirements and has been providing Genomics England with data flexibility, performance at scale and security since the project started in 2013.

Ignacio Medina, Head of Computational Biology Lab HPC Service, University of Cambridge, and Head of Bioinformatics Databases at Genomics England has been building many of the applications that sit on top of MongoDB. He said:

MongoDB is performing beautifully for us. From the beginning of the project it’s been fantastic for our developers to build and iterate quickly. Now that the 100,000 Genomes Project is running at scale, MongoDB is also helping us extend that great experience on to the scientists and clinicians who access the data, making it easier and faster for them to find critical insights in the data.

Two of the important projects also utilising MongoDB are Cellbase and OpenCGA (Computational Genomics Analysis). Cellbase is a data warehouse and open API that stores reference genomic data from public resources such as Ensembl, Clinvar, and Uniprot. By relying on MongoDB, Cellbase can typically run sophisticated queries in an average of 40 milliseconds or less, and complex aggregations in less than one second – down from six hours using previous filesystem-based querying and storage. Importantly, it can annotate about 20,000 variants per second, making it compatible with whole genome sequencing data throughput requirements, while also returning a rich set of annotations that helps scientists better understand the data.

OpenCGA aims to provide researchers and clinicians with a high-performance solution for genomic big data processing and analysis, and the platform includes detailed information on genomic material. This means OpenCGA has the ability to process incredibly complex queries based on a huge variety of variables. By using MongoDB, OpenCGA enables researchers to query data in a wide variety of ways, using MongoDB’s secondary indexes – from compound indexes to query data across related attributes, text search facets to efficiently navigate and explore data sets, and sparse indexes to access highly variable data structures.

Dev Ittycheria, President and CEO, MongoDB, concluded:

The 100,000 Genomes Project hits home for me in a very personal way as I recently lost my mother to cancer. I am extremely grateful that so many brilliant people are dedicating their time and energy to this important project. We are honoured that MongoDB is playing an essential role as the underlying data platform to produce data science that is likely to change the lives of millions of people, including someone we may personally know, for the better. This is the kind of project that inspires us to do our best work every day.

Find out more about MongoDB on their website.

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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Rare Disease Day – embedding patient experience at the heart of rare disease research

As the world marks Rare Disease Day on 28 February, Genomics England explores patient and clinical perspectives of rare disease.

In this blog we hear from Rebecca Middleton − taking part in the 100,000 Genomes project’s rare disease programme and Vice Chair of the Project’s Participant Panel.

In an accompanying blog we hear from Dr Richard Scott, Genomics England’s Clinical Lead for Rare Disease. While coming at the rare disease experience from different directions, they share the idea of progress, challenges – and hope.

Embedding patient experience at the heart of rare disease research

“I was sat drinking tea at my uncle’s wake nearly five years ago when the penny finally dropped. My maternal uncle had died due to a ruptured aortic aneurysm a week earlier; he was 62. Five years earlier my mother had died at the age of 59 of a brain haemorrhage due to a ruptured cerebral aneurysm. Talking to my relatives at the wake, my cousins and I started to pull the pieces together of the most unfortunate puzzle. We realised that a further two relatives had died of complications due to aneurysms, both aortic and cerebral, including my maternal grandmother.

We all fell silent as we realised that an unfortunate coincidence was, in fact, looking like an unfortunate flaw in our genes. After further research and talking to many experts in the field, I finally underwent a brain scan in 2014 to discover that I too had a brain aneurysm and the genetic flaw continued down our family line.

My small aneurysm is in a difficult position which means it can’t be treated without big risks, so I undergo regular monitoring and learn to live with the anxiety it brings. Along the way, I was diagnosed with familial aneurysm syndrome, a broad-brush label for an unknown fault in my genes.

Since this discovery, I have been on a remarkable journey. After existing NHS genetic testing didn’t find the answers I was looking for, I was recruited onto the 100,000 Genomes Project, became a participant on my local project delivery board in Leicester and Vice-Chair of the national 100,000 Genomes Project Participants Panel.

I am incredibly proud to sit on the local and national panels, which are at the heart of Genomics England. The Participants Panel is made up of participants from both the rare disease and cancer parts of the project and works incredibly hard to ensure our interests are represented and our valuable data used responsibly by the medical and research community.

Rare disease is complex and so is living with it. There are over 6,000 rare diseases, often presenting themselves in their own unique way. Today, one in 17 of us is living with a rare disease and each of us has had a very different and difficult journey to the door of our genetic counsellor or hospital consultant.

Rare disease day this year throws a spotlight on the patient’s involvement in research. A place where we should naturally be. It’s our ‘uniqueness’, experience and knowledge of our own disease that makes us the best placed experts to work with researchers to move medicine and understanding forward.

And that means more than being told about research, but rather being an active player in how it is developed, carried out and reported. As technology and the optimisation of big data progresses, it becomes critically important that we, as patients, work with researchers and the medical community to design research that answers our critical questions. We should be seen more than a sum of our symptoms; our voices not lost in the 3.2 billion letters of our genome.

I’m pleased to say that the national Participants Panel of the pioneering 100,000 Genomes Project reports straight to the project’s governance board. We have a loud voice at the top table. It is ground-breaking patient involvement for a ground-breaking project. We are not ‘token’ patients but have helped deliver real change for the benefits of patients and their carers already, with the support of the project team.

As the NHS aims to bring genomics from the side-lines of medicine to the mainstream by the end of the year, there is a real opportunity and appetite for meaningful patient involvement at every level of the service.

For myself and many others, research means hope. As we often have little control over our disease, it is that hope that keeps us searching for answers for ourselves and our families – or in my case for the sake of my two beautiful, young daughters. By active and effective involvement of patients in rare disease research and service design, we too can move forward from the side-lines and be central to finding future cures, treatments and better care for families. Through involvement, we become an asset as well as a patient. Let’s make that hope a reality.”

Rebecca Middleton is Vice Chair of the 100,000 Genomes Project Participant Panel.

Rare Disease Day – rare diseases aren’t rare

In this blog Dr Richard Scott talks about the long path to diagnosis for many people with rare diseases, and the challenge of raising awareness amongst the public and healthcare professionals.

As the world marks Rare Disease Day on 28 February, Genomics England explores patient and clinical perspectives of rare disease. In an accompanying blog we hear from Rebecca Middleton on how through the 100,000 Genomes Project, patient experience is being placed at the heart of rare disease research. While coming at the rare disease experience from different directions, they share the idea of progress, challenges – and hope.

Rare diseases aren’t rare – so it’s important we focus on them

Rare Disease Day was first launched 10 years ago by EURODIS − an alliance of patient-driven organisations in Europe. It’s now a worldwide phenomenon.

Why the focus on rare diseases you ask? Are there not more mainstream problems to focus on? Well, the name is misleading. Rare diseases are individually rare − by definition − affecting less than 1 in 2,000 people. But there are an estimated 6,000 or so of them, meaning that they are collectively common: an estimated 1 in 17 of us is affected.

Rarity brings with it problems, but they don’t stop there. At least half of rare disease affect children. And their impact is often severe – sadly, 30% of those with rare disease die before their 5th birthday. The impact on health and normal life is often substantial, even in those less severely affected. The diseases are typically lifelong and often affect multiple organ systems of the body.

In the ten years since the launch of Rare Disease Day, there has been much progress. There has been increasing recognition of the importance of rare diseases and increasing focus of governments and health systems. In the UK, the Department of Health issued a Rare Diseases Strategy in 2013 and will today issue an update on progress.

The long path to diagnosis – the so called ‘diagnostic odyssey’ – has been a major area of focus. It needs to be. Surveys show that it takes an average of five years to receive a diagnosis and 40% of patients are misdiagnosed.

Most rare diseases are thought to have genetic cause and the great advances in genomics in recent years are helping. Now it can cost as little as $1,000 to sequence a whole genome, although that doesn’t include the costs of interpreting the data and generating a clinical report. Other forms of genetic testing are cheaper too.

In the UK we are lucky to have access to whole genome sequencing for rare disease patients on a research basis through the 100,000 Genomes Project, on which I work. We’ve now reached the half way mark in the project, having sequenced over 50,000 genomes, and are working closely with NHS England to develop the systems that will allow genome sequencing to enter mainstream diagnostic use. This will again place us right at the forefront of rare disease genomics − but that shouldn’t make us complacent.

Even with the very best technologies available, rare disease diagnostics remain hard. In many settings, the majority of patients remain undiagnosed. Our knowledge is advancing rapidly, but is still far from complete. We all carry hundreds of rare genetic variants and it can be challenging to spot the variant that is the cause of a person’s rare disease, even if it’s in a well-known gene.

In the UK we have a long history of close work between genomics laboratories and clinicians. This new era of genomics will require even closer laboratory-clinical working to ensure we fully harness the extraordinary potential of the technologies we now have in our hands.

In the context of these great scientific advances, some of the biggest challenges we face may seem prosaic. Simply recognising that someone might have a rare disease is often challenging. How do we make the public and primary care and front line mainstream medical teams aware of these individually rare conditions?

By raising the profile of rare diseases as a whole, efforts such as Rare Disease Day are already beginning to have an effect. Broader education of the medical workforce about genomics is also helping. But there’s a long way to go and other approaches will be necessary. Increasing integration of genomics services with mainstream specialties is vital. With increasing use of electronic health care systems, there are also great potential benefits from building systems that highlight the need to consider rare disease or refer for a specialist opinion.

But rare disease care is about far more than just testing and ending the diagnostic odyssey. Coordination of the complex care of rare disease patients is often challenging, but is essential for high quality care and can bring considerable psychosocial benefits and cost savings. Currently, many patients and families bear the burden of the task. This is an area in need of greater investment.

With most rare diseases hard to treat, even when a diagnosis is made, research must be at the core of the care we offer. And with the number of people with each disease so small, patients’ wishes to share their data broadly must be heeded.

While we should be grateful that there is an increasing patient voice bringing us events such as Rare Disease Day, the drive of patient groups shouldn’t be taken for granted. You don’t need to hear many stories of patient-led research initiatives to realise that the onus is on the medical and pharmaceutical communities to keep pace with the endeavour of those affected with rare disease.”

Dr Richard Scott is Genomics England’s Clinical Lead for Rare Disease

UK leads the world as 100,000 Genomes Project hits the 50,000 genomes landmark to transform NHS patient care

The Department of Health and Social Care, NHS England and Genomics England today announced reaching the 50,000 whole human genome sequences landmark within the 100,000 Genomes Project.

It is a milestone that sets the UK on track to fully realise the potential of genomic medicine, deliver better care for patients and establish the UK as the global ‘go to’ destination in the fast emerging genomics sector.

Genomics England was established in 2013 as a wholly owned company of the Department of Health and Social Care by the Secretary of State, Jeremy Hunt. It is tasked with the delivery of the groundbreaking 100,000 Genomes Project, which is sequencing 100,000 genomes from 70,000 people, focused on patients with rare diseases, their families, and patients with cancer.

In stimulating genomic research and discovery, Genomics England aims to improve patient care and establish the UK as the centre of the global genomics industry.

Achieving the 50,000 genomes landmark has only been made possible through the generous participation of tens of thousands of patients and their families – taking part in a Project at the edge of known science. Staff in NHS Genomic Medicine Centres (GMCs), as well as those in Northern Ireland, Scotland and Wales, have worked tirelessly to not only deliver the Project, but in many cases, also pioneered totally new systems, processes and procedures to ensure that genomic medicine can become part of routine NHS care.

The project is already changing the lives of patients with a rare disease – often providing diagnoses for the first time after years of uncertainty and distress (known as the diagnostic odyssey), as well as working towards reducing costs to health and social care budgets. In cancer, significant progress has been made in tackling the global challenge of extracting of DNA of sufficient quality for whole genome sequencing – leading to significant redesign of tissue handling in the NHS.

The scope and scale of the 100,000 Genomes Project, unparalleled anywhere else in the world, has been made possible through the UK’s unique asset − its National Health Service. The NHS, as the single biggest integrated healthcare system in the world, is able to link lifelong healthcare information with whole genome sequencing data. It is a combination that brings benefit to patients whilst also demonstrating the UK’s competitive advantage in enhancing understanding of diseases, and developing products for earlier detection and treatment.

Health Secretary Jeremy Hunt said:

“This incredible achievement shows once again why the UK is a world leader in genomic medicine.
“We’re backing our world-leading scientists and clinicians in the NHS to push the boundaries of modern science and embrace new technology – using data to transform the lives of patients and families through quicker diagnoses and personalised treatments.
“It is testimony to the hard work of the clinicians and scientists across the NHS and volunteers for the project that we can continue to harness the very best of the NHS and remain at the forefront of this pioneering field.”

Genomics England Executive Chair, Sir John Chisholm, said:

The 100,000 Genomes Project was a stunningly ambitious project when announced by the (then) Department of Health five years ago. Since then Genomics England and NHS England (now joined by Scotland, Northern, Ireland and Wales), working with a huge number of ground-breaking partnerships, have built the infrastructure and protocols to deliver health-enhancing diagnostics from consented patients with undiagnosed rare genetic disease and common cancers, while at the same time enabling their data (in de-identified form) to provide the basis for research leading to improved therapies and treatments. Having built the platform and reached the 50,000 halfway point we are now able to operate at a scale to complete the target by the end of 2018.

Professor Sue Hill OBE, Chief Scientific Officer for England and Senior Responsible Officer for Genomics at NHS England, said:

This is an important milestone for the project and has only been possible because of the contribution and commitment of the participants in the project and their families.
“The milestone also marks how healthcare professionals from across the NHS have come together to transform care for the future, demonstrating how this technology can be utilised as part of routine care to improve patient lives and keep the NHS a world-leader in this important area of medicine. Working together patients and professionals have achieved so much and I would like to say a personal thank you to each and every one for playing their part.
“We are on track to complete recruitment to the Project this Autumn and, from then, the use of these cutting-edge genomic technologies will be embedded in the NHS through the new Genomic Medicine Service offering real benefits to patients and healthcare delivery.

Francis deSouza, President and CEO of lllumina (the 100,000 Genomes Project’s sequencing partner), said:

This important milestone in our partnership with Genomics England marks a significant step towards delivering whole genome sequencing at scale into the NHS and provides physicians with the data to make diagnoses based on a patient’s genome that will lead to better health outcomes.

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