Category: Genomics England

Tribute to Professor Maria Bitner-Glindzicz

We are desperately saddened to learn of the tragic death of Professor Maria Bitner-Glindzicz.  Maria was an outstanding clinical geneticist and champion of people with syndromic hearing loss.

In the 100,000 Genomes Project she was one of the earliest colleagues to be involved with the programme and a wonderful contributor. Her kindness, indefatigable enthusiasm and wisdom was unwavering and she will be greatly missed by her patients, family and all of us.

Our deepest condolences and our hearts go out to her family, her colleagues and patients.

New public dialogue on genomic medicine begins

Genomics England is beginning a dialogue, with support from Sciencewise, to explore public aspirations, concerns and expectations about the development of genomics and genomic medicine in the UK. It will bring up to 100 members of the public together with clinicians, academics and industry to discuss in depth the science and issues of genomic medicine.

What is genomics?

Genomics is behind what’s known as ‘personalised medicine’. Information about an individual’s genetic make-up is used to predict, diagnose and treat disease and ill health in the way that will work best for that individual.

Genomic medicine relies on being able to compare an individual’s DNA against that of tens or hundreds of thousands of other NHS patients with the same condition. The information returned is not only relevant to the individual but to members of their family too. The concept of sharing health data for both individual and collective good is already well understood and has been embraced by many patient groups, and reflects the founding principles of the NHS. However, it is a concept which is still unfamiliar and potentially worrying for the wider public.

Why a public dialogue now?

One of the key recommendations in the Chief Medical Officer’s annual report ‘Generation Genome’ published in 2017 was that “Genomics England and NHS England engage in an extensive public dialogue on the shared social contract between patient, public, clinicians and academics in relation to genomic medicine.”  Genomics England are keen to deliver this, building on their previous engagement work in the ‘Genomics Conversation’.

This dialogue takes place at an important time for the 100,000 Genomes Project, run by Genomics England and NHS England. By the end of 2018, the Project will have sequenced 100,000 genomes from 70,000 NHS patients affected by either rare disease or cancer. Beyond this, the ambition is to embed genomic medicine into the NHS so that it becomes part of routine care and treatment so that everyone can benefit.

Discussing all the ways that the genomics rollout could work will involve in-depth discussions with the public. They will need to consider detailed information, and engage with some complex scientific ideas.  A dialogue process lets us bring the public together with experts to explore the issue in detail, giving us richer findings than shorter focus groups or a survey.

Genomics England’s Head of Engagement Vivienne Parry said

Your genome contains information that may be important for you and your family’s health. But it can also benefit the health of other NHS patients. This is because all genomes contain clues about disease and ill health. The more genomes that can be studied, the more likely the chances of finding those clues. This is one side of the coin – what you can do for others. But the reverse is what others can do for you. Your genome can only be understood by comparing it to the genomes of many other NHS patients – the more there are, the better for you and your family.

It is this and other issues that we really want to explore through this dialogue, which will not only help us to make genomics part of routine NHS care, but keep the UK at the forefront of this remarkable technology, and make sure that we have the right ethical and regulatory environment for it to thrive.”

How will the outputs be used?

The outputs from the project will feed through directly to the work already underway to develop genomic medicine as part of routine NHS care and ensure that policy makers have a more solid foundation of information to inform next steps and to move policy making forward successfully.

It will also provide clarity on the understanding of the concept of a ‘social contract’ between the NHS and those that use it, allowing further development on the principles.

It will also shape the language and messages used.

How will the dialogue be structured?

The project will last for 8 months, and involves a rapid literature review, a stakeholder workshop, reconvened public dialogue workshops with up to 100 members of the public across three locations, followed by a Summit bringing together many of the participants with stakeholders to evaluate different futures for genomics and the NHS.

An oversight group will bring independent scrutiny to the project, and will help Genomics England develop materials for the public to use in their workshops. It is made up of a range of people who will bring different perspectives and expertise.

Chairing the oversight group is Dr Anna Middleton, Head of the Society and Ethics Research Group at the Wellcome Genome Campus in Cambridge. She said

This public dialogue is a really important part of ongoing work to understand how society is responding to, and what expectations the public have, about genomics. We know that general public awareness and understanding about genomic medicine is quite low. But what I want us to gain through this dialogue is a picture of what public expectations might be, and in particular what patients using the NHS think they should offer in return for their healthcare – their side of this ‘social contract’.

Do we expect to be able to take from a free publicly-funded service without allowing our data to be used in research? Is it altruism that is driving this? Should we have a choice in who we allow to use our data? I’m looking forward to finding out.”

The dialogue process is being designed and managed by the Ipsos MORI Social Research Institute, following a mini competition organised via the Sciencewise framework of dialogue delivery contractors.

URSUS Consulting have been appointed to evaluate the project.

Find out more

We will be posting updates on the project on the Genomics England website.

For further information on the public dialogue, please contact

Diversity of debate: the Discovery Forum comes of age – a blog from Joanne Hackett

The Genomics England Commercial Team at the Discovery Forum.

The 3rd Discovery Forum took place on 12 July 2018, bringing together hundreds of people from across the industry sector. Chief Commercial Officer Joanne Hackett writes down her thoughts about the day.

There’s great satisfaction in watching something we have helped to create develop a life and personality all of its own – which is why I took huge satisfaction at the Genomics England Discovery Forum on 12 July.

The Forum grew out of our original GENE Consortium, which provided valuable learning about how to align the interests of industry, research and public. But no matter how useful GENE was, we knew it had served its purpose. It was time to build a successor that broke down traditional silos and created a platform that could truly integrate industry into the process of accelerating discovery, speeding translation from the lab to the clinic, and catalysing the UK genomic sector.

And so, in July 2017, the Discovery Forum was born. Initially with a handful of key industry players, it now boasts 69 members – and it’s still growing. Membership encompasses the A to Z of genomics (well, the A to W − from AstraZeneca through to the Wales Gene Park).

The July 2018 Forum brought together over 100 representatives from every aspect of the genomics sector – from patients to researchers to funders to data analysis companies to software specialists to sequencers to biopharma businesses, and everything in between.

I was particularly proud to see participants of the 100,000 Genomes Project here. These are the people whose generosity – often in difficult circumstances − is making genomic discovery possible, and who have made a huge contribution to the new NHS Genomic Medicine Service which rolls out later this year. Their experience, insight and commitment are a keystone – without them, the Discovery Forum simply couldn’t work.

And everyone comes to engage – italics used for emphasis – because the Discovery Forum isn’t some pointless talking shop. It is a real platform for debate, where attendees openly discuss challenges and solutions. There is no showboating, axe-grinding or agenda setting. It’s where the genomics business gets down to learn about the business of genomics.

Just looking at the breadth of topics we covered in a single day shows us its value: the targeted collection of multiomics (-omics); differing attitudes to hypothesis generation; considering samples as data; the costs of storing massive amounts of data; potential futures for Genomics England; and much more besides.

It is this diversity of debate that makes the Discovery Forum a truly unique resource. Where else… what other forum… brings together so many people from so many different fields on a regular basis? Where relationships, understanding – and ultimately mutual trust in motivations – are built up over time?

Just one year ago I didn’t dare to dream that the Discovery Forum would come so far so fast – and certainly not that it would have come of age on its first birthday. It really is developing a life and personality all of its own − and I’m genuinely intrigued to see where it takes us.

Consent and participation in the 100,000 Genomes Project – public attitudes

A new public dialogue on attitudes to sharing personal data as part of research has used the 100,000 Genomes Project as an example of best practice in obtaining consent.

The way that Genomics England obtained consent from participants in the 100,000 Genomes Project was praised by the public focus groups who took part in the project, run by the Health Research Authority (HRA) and Human Tissue Authority (HTA), who are now considering how best to use Genomics England’s approach as an example of good practice for future work and guidance for researchers on gaining consent.

The HRA and HTA commissioned Ipsos Mori’s Public Dialogue Centre to better understand more about the public’s awareness of the importance of donated tissue being linked to patient health data, and to learn what reassurances the public may need in order to provide their consent.

As part of the public dialogue, participants in a series of focus groups were invited to hear more about the 100,000 Genomes Project. Whilst participants had a limited understanding of the science behind the project, they were positive about the work once they’d seen a video – one of a number commissioned by Genomics England as part of the consent process for potential participants – explaining the technology and its benefits.

The focus group participants found that the wording was simple and positively constructed, and it was felt this would help potential participants in the 100,000 Genomes Project to digest the information, and have a reasonable understanding of what consent would involve. Participants liked the fact the form listed different types of health data which can be accessed, and they also liked the discrete sections.

The HRA/HTA report also details a number of constructive comments from focus group participants on how the consent process could be made clearer and more useful, which will be used to further improve the consent model.

Professor Mark Caulfield, Genomics England’s Chief Scientist, said:

“Our entire project is founded on informed consent from our participants who agree to take part. We have been careful from the outset to ensure that our consent process is comprehensive and rigorous, and includes leaflets and videos that describe what their data will be used for and by whom. We’re pleased with this feedback, and the opportunity this report provides to reflect and further improve our consent model as genomic medicine becomes more embedded in routine NHS care. We look forward to contributing further to this ongoing piece of work with the HRA and the HTA.”

The HRA / HTA public dialogue was supported by Sciencewise and The Department for Business, Energy, and Industrial Strategy (BEIS). The final report can be viewed on the HRA website.

Director of Communications for Genomics England, Katrina Nevin-Ridley said

“This report is a detailed look at public views on the various different ways in which informed consent can be gained for research. It is a welcome addition to our ‘Genomics Conversation’ which helps us to understand how, and in what circumstances the public are happy to provide their health data for research. As part of the conversation, Genomics England is carrying out further public dialogue that will help inform the development of a national genomic medicine service.”

Genomics England has also published a report on the views of black African and black Caribbean communities on participation in the 100,000 Genomes Project. Other activities planned include a series of regional ‘future debates‘ on whole genome sequencing with the British Science Association, events in partnership with the Progress Educational Trust, and a survey of people with rare and genetic conditions in collaboration with Genetic Alliance UK.

As the NHS celebrates 70 years Genomics England sequences its 70,000th genome

As the NHS celebrates its 70th birthday, Genomics England announces that it has now passed the 70,000 genomes mark. This milestone comes just five months after the 100,000 Genomes Project reached its halfway point – signalling that it is well on track to reach its goal of 100,000 genomes by the end of this year.

Genomics England has worked with the NHS to create the biggest national genome sequencing project of its kind in the world. It has provided the evidence NHS England needs to embed genome sequencing in routine care through the new Genomic Medicine Service (GMS). Rolling out in October 2018, the GMS will help to ensure that the NHS stays at the forefront of healthcare delivery – now and in the future.

The groundbreaking 100,000 Genomes Project focuses on patients with rare diseases, their families, and patients with cancer. Working with sequencing partner, Illumina, Genomics England has now sequenced a total of 71,095 genomes.

Beyond 2018, Genomics England will continue to support the NHS GMS, acting as a testbed for new applications, encouraging discoveries and their translation into novel medicines and treatments, as well as working to support a thriving genomic medicine industry in the UK.

Health Minister Lord O’Shaughnessy said: “Genetic sequencing can revolutionise healthcare by offering truly personalised care to patients and their families.

“This project is a shining example of a partnership between the public sector, the life sciences industry and the research community – with NHS patients reaping the benefits.

“Genomic medicine is no longer a thing of the future, it’s here now and helping to save lives.”

Professor John Mattick

Genomics England’s CEO, Professor John Mattick, said: “Genomics England’s mission is to realise the enormous potential of genomic information to enable precision medicine.  As the technology and our understanding continue to grow over the coming years, we will provide genome analyses to inform personalised treatments and preventative actions tailored to individual circumstances, to ensure the best healthcare for our patients and generations to come.”

Professor Dame Sue Hill, Chief Scientific Officer for England, who is leading the NHS Genomics programme, said: “I’m delighted the Project has reached the 70,000 sequence mark in the week of the 70th Birthday of the National Health Service. The NHS has harnessed cutting-edge science and technology through the Project to deliver real benefits for patients with rare diseases and cancer and in the growing field of genomics and health we are, once more, building a world-leading service that is admired and respected across the globe.

“Reaching the 70,000 mark has been possible because of the contribution and support of all the patients and families involved and driven by the tremendous work done by the dedicated teams across the NHS in our Genomic Medicine Centres in providing the highest quality samples and data as part of routine care.”

Professor Mark Caulfield, Chief Scientist at Genomics England, said: “Genomics England was set up five years ago during the 65th celebrations of the NHS. The 100,000 Genomes Project is ground-breaking and on the 70th anniversary of the NHS it is amazing that we have now sequenced over 70,000 genomes from participants with rare disease and cancer – and we are grateful to everyone who has generously taken part in the Project. It has already changed the lives of many patients with cancer or a rare disease in the UK, and now this programme will expand to further transform genomic health in the NHS with improved outcomes for many more.”

A New Deal on Data – articulating the contract between science and people

By Anna Middleton (Head of Society and Ethics Research at Wellcome Genome Campus), Vivienne Parry (Head of Engagement at Genomics England), Julian Borra (Citizen, Founder of Thin Air Factory)

Are you with us?

For most of us it is hard to unpick the various declarations, assurances and guarantees made regarding the sanctity of our data. Even the General Data Protection Regulation still feels quite far removed from the everyday lives of ordinary people and is seemingly absent of any consultation with them. People need to both see and hear proof that they’ve been listened to. And they will act against anyone who seems to wilfully dismiss or disregard them – with every right to do so. With Facebook recently under the spotlight, there is tangible alarm about the use of our personal information by others. A breach of confidence or inappropriate access to data becomes really sensitive when we consider our most precious and personal information. In a health sense, what is more personal than our DNA? It’s what makes us ‘us’.

We broadly know that scientists, clinicians and academic institutions collect, store, research and share DNA and medical information as part of the global endeavours to understand human health and treat human suffering. As part of this endeavour DNA information bounces around the Internet on an unbelievably massive scale, in ways unknown to the person who donated the data.

We probably expect ‘science’ is gathering, storing, analysing and sharing our data with respect, transparency and integrity. Whilst we hope that there is choice in this and we hope that we have actively consented, have we ever really discussed this as a collective society? Is this even possible?

Is it widely known that particularly for genetic research it is only possible to interpret what a glitch in DNA means if there are hundreds of thousands of DNA glitches from other people to compare it to. So, Big Data and DNA go hand in hand and are necessary for genomic medicine to deliver on its promises.

But, if science is truly going to serve humankind in the best way possible we need to be clear on the terms of the interaction and transaction with people, on their terms. And to do that we need a simple and clear conversation; to be certain that we can fulfil their demands or at least understand their desires and concerns.

The need for a PEOPLE POWERED conversation

The why?

A: The world of data is leaky

B: Society’ hasn’t yet been part of a clear conversation

When thinking about A we have to be honest. Nothing is perfect. No data is 100% secure. No system is flawless. No regulation is absolute. No cache of information is 100% bullet proof – and if anyone promises that, they’re over promising.

This is a given that we have got to accept.

The type of data we are talking about here is the purest most precious kind, fundamental to our identity and existence. DNA and linked medical data – the foundational stuff that makes us who we are. Whilst our data might be ‘de-identified’, i.e. our name and address has been uncoupled from it, ‘anonymity’ cannot be absolutely guaranteed, because health information can always be linked to other personal information that is also on the web, and in our increasingly data-connected world, it is entirely feasible that we could, in theory, be identified from our DNA alone.

Which brings us to the B.

There are a lot of companies and regulatory bodies that broadcast commitments and assurances about data use. But as there has been no collective societal ‘sign up’ – so the pronouncements and commitments could be seen as one-sided. Aside from (relatively small scale) targeted engagement initiatives, there hasn’t yet been a global two-way conversation. No complete consultation. No reciprocity. No serious voice given to the most important people and the principal recipients of the good works undertaken with their data.

This is especially problematic when it comes to trying to get more people to share their precious DNA – their genome – to advance medical research and progress healthcare. Which is why the scientists need to ‘go first’ with starting this conversation.

The crunch

To move forwards we need:
• the medical, clinical and academic institutions and the policy makers to clearly articulate the assumptions behind ‘people’s best interests’ and make this available for debate.

• society to accept the tiny risk inherent in sharing their data with individuals, organisations

We need the people on both sides to be in this together – mutually accepting and supporting the power of precious data sharing to make life better.

Going Forwards

Drawing up the New Deal

Simplicity is key. Two clear parties. Two clear beneficiaries. And equally mutual rewards.

Consultation

This is a reciprocal people-powered deal that brings both sides together for better. And the people’s voice must be consulted, heard and written into it. This will require a comprehensive consultation process involving ordinary people from all walks of society.
This should involve Qualitative and Quantitative explorations and interrogations of the topic and the terms of the deal. It should involve experts in large-scale, population engagement techniques.

How do we start the conversation?

We need a starting point for that conversation – an ‘in’; and starting with the genome isn’t it. We know from our own research that the vast majority of the broader public have not yet encountered the term. However, more than 90% of the public are online and feeding their data into the grid. Thus ‘data’ is the conversation starter that can take us to DNA.

The binary algorithms that once sat invisibly inside tech tools that serve humanity –- have now become visible – data has become a ‘thing’. Something we can point at, hold up, scrutinise and hold accountable. Data and its big brother, Big Data, are now discussed, interrogated and judged everywhere from the Senate Commission to Mumsnet.

So, Data; our relationship with it; and with those who harvest, explore and administer it ‘on our behalf’ gives us a rich area from which to begin.

The conversation needs to focus on how science and humanity collaborate and win, together.

Communication

Language and Tone are everything. Pub and school gate rules apply (i.e. it can be discussed anywhere and everyone can participate). This is a People Powered Deal. Not a Protocol. This is a simple deal that respects and honours every human’s right to control their own data destiny. And confidently go into an agreement where they believe that the terms will be upheld to the best of everyone’s ability. Which means it must be couched in clear simple terms.

Distribution

We need the New Deal to be visible to all at every level. This will require a robust channel strategy – so we would also need to test best channels for spreading the word. And answer some pretty simple questions: Is it an event based news worthy event? Is it a web based platform for commitment with visible partners? Is it a socially driven call for better – a clarion call where we give the New Deal to the people and get them to use it as a lever to agitate for better – a movement.

We feel it is time for science and policy to scrutinise their direction of travel – with less rhetoric about the benefits of research and delivery of science (i.e. going in one direction from them to us) and more about serving humankind, recognising that we are all in this together. We, collectively are a partnership and we need the people of society to feel they sit with the scientists so that the journey into human discovery is one made together.

New genomics education and training resources from the Royal College of General Practitioners

Dr Jude Hayward and Dr Imran Rafi are Co-Clinical Champions for the Royal College of General Practitioners’ Genomics in Primary Care Programme. Here, they highlight resources created by RCGP to help general practitioners understand the impact and applications of genomics in primary care. 

Genomics testing is increasing and growing numbers of patients are likely to present to their GP practice, as the gateway to NHS care, with issues and questions relating to themselves or family members. Genomics is already impacting in Primary Care in the fields of cancer and rare disease, altering the management of patients through improving diagnosis, risk prediction, prevention and treatment. The influence of genomics in prescribing and management of infectious disease in primary are potentially just around the corner.

With funding from Health Education England’s Genomics Education Programme, the Royal College of General Practitioners (RCGP) has created educational and training resources to ensure that the workforce of today and the future is equipped to respond to fast-paced developments in genomics. These are based on outputs from the programme’s Primary Care Strategy identifying only those knowledge and skills required by primary care, avoiding overburdening with information. The College has published a four-part webinar series on familial cancer, rare disease, non-invasive prenatal testing (NIPT) and ethics. There is also a three-part podcast series with an introduction from RCGP Chair, Professor Helen Stokes Lampard. Podcast topics include genomics terminology, application of genomics in primary care and ethical, legal and social implications of genomics in primary care, including direct-to-consumer testing and pharmacogenomics.

To learn more, visit the RCGP and Genomics Education Programme websites.

Meet Professor John Mattick, CEO at Genomics England

Professor John Mattick joined Genomics England as its first Chief Executive Officer on 21 May – coming to us from the prestigious Garvan Institute of Medical Research in Australia. Genomics England speaks to its new CEO to discover more.

What first sparked your interest in science?

I had a wonderful science teacher in secondary school, who led me to love the subject. I was something of an aspiring polymath, having studied and done well in English, Mathematics, Science, Latin and French in the Australian equivalent of my GCSEs, and was disappointed that I could not do English and Philosophy along with my Science course at university. I had decided to do Science, rather than an applied course like Medicine or Law, as I thought it would be more interesting, and suit my soul. In any case, I have always maintained my love of literature, language, music and philosophy, and have branched out into history as well.

What made you specialise in genomics?

In second year of my science degree, I did Biochemistry and Genetics, which I embraced. I was fortunate to begin my PhD in 1972, the year in which gene cloning was invented, and to become part of the pioneering generation of molecular biologists. I have always viewed biology more in informational than chemical terms, hence my attraction to genomics, which is molecular genetics writ large. And I was fascinated by the challenge of understanding how 3 billion bases of DNA, just 6 gigabits in informational terms, manages to produce a walking, thinking human from a single cell – surely the most sophisticated information suite in the world, and not to be thought of in primitive terms.

What led you to the clinical side of genomics?

It has been clear to me for many years that genomic information, integrated with clinical and other data, would lie at the centre of the future of both biological discovery and healthcare, and that the clinic and research would fuse into one – with humans, not model organisms, at the centre. It has intrigued me that many colleagues in biomedical research, which has been traditionally focused on molecular and cellular biology, have been slow to fully appreciate the importance of genomics. Indeed, this was my motivation to accept my previous position as the Executive Director of the Garvan Institute, which was on the understanding that I would promote genomics and informatics both in the laboratory and in the clinic. I hope to take this a lot further now, in collaboration with many partners in the UK, which has leads the world.

As the recipient of many awards and honours, what would you say was your biggest achievement?

I think my most important professional achievement has been to be the first to recognise that the human genome is not largely junk, but rather (that the 98.5% that does not code for proteins) specifies a massive hidden layer of regulatory RNAs that organise our development and provides the platform for brain function. This explains many mysteries, including the fact that the human genome contains the same number (20,000) and largely the same repertoire of conventional (protein-coding) genes as simple nematode worms with only 1,000 cells, so the information that produces a human must lie elsewhere. If correct, this is a huge development in the understanding of the human genome. While not everyone yet agrees with me, the evidence is very strong and my thesis is more widely accepted than it once was. The problem is that this is not a simple ‘discovery’ that can be easily validated, but a major change in the way the genomic programming of complex organisms is understood, which runs contrary to the protein-centric conceptual framework that has dominated molecular biology and the textbooks since the 1960s, which has been hard to shift.

Other personal achievements have been the establishment of the Institute for Molecular Bioscience in Brisbane, the model and forerunner of many outstanding institutes that have established that city as a major centre of research and innovation, the Australian Genome Research Facility as a national centre for DNA sequencing and analysis, and later the development of the Garvan Institute as a global leader in clinical genomics. Of course I am also pleased with these, but I was only doing what was needed to be done.

Of course, my biggest personal achievement is three beautiful sons, and a wonderful marriage.

How has the world of genomics changed since you started your career?

The biggest change has been the spectacular development of DNA sequencing technologies over the past two decades, and the associated huge drop in the cost. Sequencing costs will fall even further in the coming years, to the point where it will be cost-effective (if it is not already) to routinely incorporate whole genome analysis into clinical decision systems and the management of health, both individually and systemically. This will accelerate our understanding of human biology, especially in relation to cognitive functions and fragilities that are difficult, if not impossible, to study in model organisms. It will revolutionise healthcare, transforming medicine from the art of crisis response to the science of good health, with massive improvements in the quality and efficiency of the healthcare system. It will also create many opportunities for industry, with flow on effects from all of these developments to national productivity and the national economy. Genomics England is leading the way, which is why I was attracted to come.

If you could give a younger version of you one piece of advice, what would it be?

Make a success of what’s in front of you, but keep looking up to make sure you are going in the right direction. Everyone is different – so follow your own lights while noting what makes others good. If you want to be a great scientist, focus on the big questions and big mysteries – the things that are not explained or just don’t make sense. Bring energy, intelligence, responsibility and integrity to everything you do. Above all, be a decent, thoughtful, kind and generous person. The world will repay you in spades.

If you weren’t a scientist, what would you be?

A writer, I think. I harbour ambitions to do just that and hope to start work on a serious but hopefully entertaining coffee table book.

And finally, what brought you to Genomics England?

Three things…

Firstly − all of the above. It very much feels like my career to date has been preparing me for this role at Genomics England.

Secondly − this is a hugely important moment in medicine. We are at a tipping point that will largely see ‘one-size-fits-all’ approaches to health consigned to the history books – and Genomics England is one of the few organisations that appreciates the scale of the revolution.

And lastly − Genomics England is ideally placed to shape the future of healthcare: to help deliver a new NHS Genomic Medicine Service; to act as a catalyst for ground-breaking research; to accelerate new discoveries into mainstream care; to make the UK the epicentre of global research, innovation and investment in the most important industry in the world; and, ultimately, to change lives for the better.

Genomics England can transform medical research and healthcare – and I will work to realise its vast potential. This is an exciting organisation at a pivotal point in its history – and I’m honoured to be here.

Response to the Prime Minister’s speech on artificial intelligence

Today, Prime Minister Theresa May will announce the Government’s plan to use artificial intelligence to diagnose cancer at earlier stages, which will reduce deaths by around 10% by 2033.

In response, Sir John Chisholm, Chair of Genomics England, said:

The Prime Minister’s commitment to the Life Sciences Strategy and the opportunities it opens for the UK is very welcome. Combining the unique strengths we have in the NHS linked to our world-class science gives us the chance to be global leaders in 4th generation technologies linked to wellness and health.

Data science and the huge advances in computing and clinical technology are already transforming the lives of patients in the UK and across the globe. 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.

Over 1,300 researchers granted access to the Genomics England Research Environment

  • The number of users with access to the Genomics England Research Environment has more than doubled since our last update in March 2018 – now over 1,300 researchers are working with data from the 100,000 Genomes Project.

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.

The first members of GeCIP were given access to our Research Environment in June 2017 to work on the de-identified data from the 100,000 Genomes Project and test the environment. Since then, the number of users has grown and this week we’re excited to announce that over 1,300 GeCIP researchers now have access to the Research Environment. These researchers are part of 25 GeCIP domains, mainly covering cancer and rare disease:

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
Cancer of unknown primary Cardiovascular
Glioma Immune disorders
Haematological malignancy Non-malignant haematological and haemostasis disorders
Melanoma Musculoskeletal
Pan-cancer Renal
Renal cell carcinoma
Sarcoma
Testicular cancer
Upper gastrointestinal cancer

See a list of approved research projects

GeCIP members currently have access to 44,067 genomes and clinical data for over 60,000 participants. This is already the largest number of whole genomes with associated clinical data anywhere in the world and excitingly, this will continue to grow with each data release as more patients are recruited to the project and more genomes are sequenced.

We have also linked our data to external datasets, such as Health Episode Statistics, Patient Reported Outcome Measures and Mental Health Services Data Set, to create a really rich resource with longitudinal life course follow-up.

All of these data are housed in the Genomics England datacentre and accessed using the Research Environment, a virtual desktop environment with all of the software and tools required to analyse the data. We hope that by providing all of these data to GeCIP members we’ll be able to gain a better understanding of disease, leading to improved diagnosis and treatment for patients.

Dr William Cross (Queen Mary University of London), a member of the Colorectal Cancer GeCIP domain, said:

Essentially I got involved in the [100,000 Genomes] Project as I am interested in trying to make sense of the vast heterogeneity we see in cancer genomes. There have been several projects like the Project (such as The Cancer Genome Atlas), but where this project is truly unique is the all-encompassing whole genome sequencing (WGS) of samples and the inclusion of clinical annotation, which is commonly missing or unavailable in other projects.

The reason WGS is so exciting is that there is a relatively unexplored world in the non-coding regions of the genome. We may very well find new types of colorectal cancer driven by mutations in RNA genes, for instance.

As for the Research Environment, I think the data are very well organised and accessible. We have been given vast resources in the form of the cluster (grid-computer) and I feel that this was a well-conceived and essential part of the project.

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