Category: Genomics England

Genomics England launches next-generation research platform central to UK COVID-19 response

British tech company Lifebit and Amazon Web Services to support a dedicated environment for researchers working on COVID-19 vaccines and treatments

Genomics England (GEL) has today launched a next-generation genomic research platform that will play a key role in the research response to COVID-19. This ground-breaking research environment will transform how genomic data is made usable for global biopharma and academic researchers. It will provide world-class patient data security, while enabling the flexibility required for research at the bleeding edge of science.

GEL has partnered with innovative British deep-tech company Lifebit and is using global cloud provider Amazon Web Services (AWS) to power the platform. The immediate focus for the research environment will be on COVID-19 data and analytics. The platform will ultimately also harness the GEL 100,000 Genomes Project data in the fight against cancer and rare diseases.

The launch of this new research environment reflects a new chapter in the role that genomic research can play in collaborative drug discovery and treatment development for the benefit of the health industry. By using AWS’s scalable and secure cloud computing and storage infrastructure in the UK, and then enabling access, analysis and collaboration through Lifebit’s unique technology platform, GEL will unleash the breakthrough potential of researchers around the world. The data stored on the platform will never leave GEL’s highly secure environment but will allow flexible research access to it. Much like the use of apps on a smartphone, researchers will be able to introduce cutting edge analytical tools of their choice, link those tools securely with their in-house data, and conduct research in private workspaces that are audited, protected and controlled by GEL’s strict information governance policies.

Data looked after by Genomics England is stored securely while enabling better analysis by approved researchers – through Lifebit’s platform.

In addition, GEL, in partnership with the GenOMICC consortium, is working with the NHS to deliver whole genome sequencing of up to 20,000 COVID-19 intensive care patients, and up to 15,000 people with mild symptoms. This data will be stored in the AWS UK Region under the control of GEL.

Lifebit’s leading platform will allow researchers to query, analyse and collaborate over these very large sets of genomic and medical data in seconds. Its enhanced functionality and automated tools will speed up researchers’ understanding of the underlying genetic factors that may explain what makes some patients more susceptible to the virus, or more severely ill when infected. Researchers’ findings will help fast-track the development of vaccines and treatments as well as identify those most at risk.

The launch of the new research environment fortifies the UK’s leadership position in genomics, with the aim of enabling global research collaboration, along with mainstreaming genomic medicine in UK healthcare in partnership with the NHS.

Chris Wigley, CEO at Genomics England, said:

This is all about impact for patients in the UK and beyond, who will benefit from GEL’s support for the response to this terrible pandemic. By improving understanding of why some patients have such severe responses to the virus while others have a mild response, GEL is helping to support vaccine and drug development. This will ultimately ensure that the treatment of the UK’s COVID patients is personalised, safer and more effective.

I am incredibly excited that Lifebit and AWS have joined us to launch the next phase of our research capabilities. Speed is of the essence and it has been heartening to see the dedication to getting this new infrastructure stood up as rapidly as possible.  Beyond the immediate focus on COVID-19, the advanced capabilities of the Lifebit and AWS environment will over time allow us to introduce contemporary bioinformatic workflows for researchers in rare disease and cancer research, unlocking the potential for the UK population genomic data to contribute to target discovery, functional genomics and advanced clinical trial design.

The Chair of GEL’s Participant Panel, Jillian Hastings Ward, said:

I am delighted that the introduction of this new technology not only makes my data more secure, but that it also makes it more useful to researchers in academia and industry around the world.  My hope is that this investment in technology is going to increase the impact that personal data is having on research in cancer, rare disease, and also in COVID-19.

John Davies, Head of UKI Healthcare, AWS Public Sector, AWS, said:

We are delighted that Genomics England has selected AWS and our APN partner Lifebit to rapidly deploy their Covid-19 research environment. Using AWS, Genomics England will be able to provide researchers with access to secure, scalable cloud computing resources that will enable them to perform studies to better understand the virus and deliver better outcomes and treatments for NHS patients.

Dr Maria Chatzou Dunford, Lifebit CEO, said:

Genomics England’s groundbreaking Research Environment changes how population genomics is done forever. GEL is widely recognised as the pioneer of population genomics and now they have architected the world’s most cutting-edge Research Environment. As a British company we are honoured to play a central role in this historic initiative and in the UK’s world-leading COVID-19 Research Response.

For the first time, we have managed to combine Fort Knox-grade security for participant data with maximum research flexibility. GEL sets a precedent on how, by using federated technology, research platforms should bring computation to the data, rather than the other way around. Now disparate cohorts of large and sensitive data can be analysed by researchers without copying or moving the data, and true collaboration can happen. Together with our existing federated deployments with big pharma and research institutions, this rings in an end to the era of risky and unnecessary data transfers.

Find out more about the GenOMICC-Genomics England COVID-19 study.

Twenty years on from sequencing the first genome

In this opinion piece, Chris Wigley, CEO of Genomics England, shares his reflections on the 20th anniversary of the first genome to be sequenced.

Not for a century has the world witnessed a pandemic on anything approaching the scale of COVID-19. Millions have been infected, almost half a million have died, economies have been shut down, jobs lost, schools closed, families divided, and civil liberties restricted to levels unknown outside war time. As the UK cautiously tip toes out of lock-down, the virus continues to wreak havoc around the world. While we can manage risk, few believe the scourge will be fully conquered without the development of an effective vaccine.

The search for a vaccine is already underway, with researchers from China, the US and Europe racing against time to deliver a response. Even when such a vaccine is available, however, a crucial factor in combating the virus’ deadly impact will lie in determining those who need it most, those who, for whatever reason, are most at risk. That will not be easy.

COVID-19 is not uniform in its impact. For all too many it has proved deadly yet for others its impact has been negligible. But why? Some correlations are clear, related to factors such as age, underlying health conditions, living standards or ethnicity for example. But for the moment they are just that, correlations – associations, not causes.

The key to cracking the conundrum lies in the science of genomics. Twenty years ago today the multinational Human Genome Project team announced that they had sequenced the human genome. They output was a diagram of every single gene, every letter of DNA within the human body.

It was, rightly, hailed as an amazing breakthrough. Bill Clinton described it as “the most wondrous map ever produced by humankind”. Scientists dreamed of the benefits that would accrue; of treatments for conditions such as cancers, Alzheimer’s, cystic fibrosis. Such treatments could be tailored to individual needs – a kind of made-to-measure medicine.

But much work remained to be done. Each genomic map was unique. What was needed was not one map, but hundreds of thousands, even millions across the world. Such a data base would allow scientists to look for fractional differences between the maps. Groups with genetic differences and  medical conditions in common would suggest an evidential link between the two. The bigger the data base, the more anomalies could be spotted, the stronger the evidence.

In July 2013 the then prime minister, David Cameron, set up Genomics England. The aim was to make more data available to health professionals, academics and others, support their research work and encourage the translation of their results into front line health care. To turn science into healthcare, using technology. One of our flagship projects was to boost the UK data base by sequencing 100,000 whole genomes. In 2018 the target was lifted to 1 million with an ultimate goal of 5 million within five years.

While more data means stronger evidence, it has also increased the importance of being able to effectively mine that data. That requires an alliance of data collection, bioinformatics and advanced analytical techniques like machine learning. But above all it requires the willingness of patients to knowingly and willingly provide the data on which the whole science of genomics rests, and ideally to engage with the research that results.

The arrival of COVID-19 has provided an added spur to our efforts. We are hard at work building up more evidence of what determines the severity of a person’s response to COVID-19. To do that, we need to examine the genomes of folks who respond really badly to the disease, and those who respond unexpectedly well (indeed, may have no symptoms at all), and compare them with the wider population.

In partnership with the NHS, the GenOMICC consortium and Illumina, we are therefore collecting and analysing the data from up to 20,000 patients who needed intensive care treatment as a result of contracting COVID-19 and up to another 15,000 who were either mild responders or asymptomatic.

The work will look at the varied effects of COVID-19 with the aim of identifying those most at risk and helping to fast track new therapies in clinical trials. If you have had COVID-19, either severely enough to be in intensive care, or mildly enough to only have modest if any symptoms – we’re looking for volunteers: go straight to our sign up page.

Twenty years ago, the researchers who manually wove that gargantuan tapestry would have gaped at the idea that we could sequence hundreds, even thousands of genomes at a time, or that those data could in a matter of weeks be available in secure workspaces for researchers around the world. The advances in technology and science, and the reduction in cost and time of sequencing, have powered a revolution over the last couple of decades. COVID-19 is now forcing another evolution, some might say revolution: driving us with ever greater urgency to deliver predictive, prescriptive and personalised health care. To bring the benefits of genomic medicine to everyone.

UK leading on patient-centric precision medicine research

A novel system which will allow rare disease patients and their caregivers to add additional information about themselves to research databases is being developed by Sano Genetics in collaboration with Zetta Genomics and Genomics England. The system will add an important layer of patient derived information to the groundbreaking precision medicine research being carried out through Genomics England. The information provided by individuals may be reported by participants directly, for example daily symptom tracking, or by a device such as a watch that measures activity or sleep.

Jillian Hastings Ward, Chair of the Genomics England Participant Panel, said:

Many patients and their families are keen to work with researchers to better understand their health conditions. Tools which enable this to happen effectively could lead to exciting new discoveries.

The project won £450,000 grant funding from Innovate UK as part of its competition, Digital Health Technology Catalyst Round 4: Collaborative R&D.

This system is a first and further cements Genomic England’s commitment to participant involvement in research.

This new initiative will lay the groundwork for better capturing additional data directly from patients and their families in the ‘real world’ to learn about disease progression and treatment effectiveness from their perspective. Collecting information about health and wellbeing directly from patients can help fill in the blanks between infrequent doctor visits. For example, wearable devices or digital journals that allow parents of children affected by neuromuscular conditions such as Duchenne Muscular Dystrophy to record daily activity would provide much more detailed pictures of disease progression, or improvement after treatment. Development of a patient platform will also enable patients to be notified about new research opportunities that may be relevant for them, including clinical trials that test new medicines.

Sano Genetics, an SME based in Cambridge, UK has developed a platform for patient engagement in precision medicine research, and is leading the consortium effort to further develop the technology for use in population-scale genomics programmes. Zetta Genomics, an SME also based in Cambridge, brings expertise in big data analysis in genomics using OpenCB, a leading open source software for large-scale genomic data management. Genomics England is a company wholly owned by the UK Department of Health and Social Care that has been at the forefront of patient partnership in precision medicine through the delivery of the 100,000 Genomes Project and the Genomic Medicine Service with the NHS. This collaboration represents another significant step in developing technologies and processes that put the patient voice at the heart of research. 

The collaboration involves two main workstreams. The first workstream involves surveys and workshops with patients to influence the features of the platform, and an ethical, regulatory, and legal working group to ensure that any proposed use-cases meet the highest standards in the United Kingdom. Two workshops were held in April with participation from more than twenty participants from the 100,000 Genomes Project and other genetics research initiatives across the UK. A survey of research participants and further workshops will be held in the coming months while the platform is under development. The second workstream is focused around technical developments of the Sano Genetics platform and OpenCB technology, including stress-testing the systems for scalability using simulated data and building capabilities for federated data analysis, whereby data can be only be analysed within ‘safe havens’ such as the Genomics England research environment.

The Innovate UK funding will allow the consortium to develop the technology, and go to market in 2021 with a patient engagement platform for population-scale genomics programmes. This collaboration has the potential to accelerate precision medicine by enabling access to real-world data and patient-reported outcomes on a population scale by making patients genuine partners in the research process.

Patrick Short, CEO of Sano Genetics, said of the partnership:

We are very excited to develop the Sano platform in collaboration with Zetta Genomics and Genomics England, and hope this collaboration can serve as a model to other research programmes and biobanks. This collaboration is initially focused on rare disease, where there is a huge need to develop new treatments and very dedicated patient groups and advocates. We believe our platform can also help accelerate precision medicine research in common genetic conditions and cancer, and are actively setting up collaborations in these areas as well.

Augusto Rendon, Chief Bioinformatician at Genomics England, said:

Collaborative efforts such as this are helping us further explore how additional data sources can be used to impact positively on healthcare, while ensuring that the highest levels of data security and integrity are met along the way.

Will Spooner of Zetta Genomics said:

Modern digital technologies enable new paradigms for participant engagement in research. The studies enabled by this and similar initiatives are set to drive significant advances in biomedical science. Advances that ultimately translate into the new precision medicines and diagnostics that will improve patient outcomes for generations to come. We are delighted to be part of this ground-breaking project that puts the participant at its heart.

New partnership to sequence human genomes in the fight against coronavirus

  • Genetic susceptibility to coronavirus to be tested in ground-breaking nationwide study
  • Genomes of thousands of patients with coronavirus will be sequenced to understand how a person’s genetic makeup could influence how they react to the virus
  • Genomics England partners with University of Edinburgh to lead research drive to support the search for new treatments

Thousands of patients severely ill with coronavirus will have their genetic code studied to help scientists understand whether a person’s genetics may influence their susceptibility to the virus.

A major new human whole genome sequencing study will take place across the NHS, involving up to 20,000 people currently or previously in an intensive care unit with coronavirus, as well as 15,000 individuals who have mild or moderate symptoms.

Genomics England, is partnering with the GenOMICC consortium, Illumina and the NHS to launch the research drive, which will reach patients in 170 intensive care units throughout the UK.

The project is backed by £28 million from Genomics England, UK Research and Innovation, the Department of Health and Social Care and the National Institute for Health Research. Illumina will sequence all 35,000 genomes and share some of the cost via an in-kind contribution.

The study, facilitated by the University of Edinburgh and multiple NHS hospitals, will explore the varied effects coronavirus has on patients, supporting the search for treatments by identifying those most at risk and helping to fast-track new therapies into clinical trials.

Health and Social Care Secretary Matt Hancock said: “As each day passes we are learning more about this virus, and understanding how genetic makeup may influence how people react to it is a critical piece of the jigsaw.

“This is a ground-breaking and far-reaching study which will harness the UK’s world-leading genomics science to improve treatments and ultimately save lives across the world.”

Since genetic discoveries need very large numbers of patients, the GenOMICC study ultimately aims to recruit every single COVID-19 patient who is admitted to intensive care in the UK.

Patients will only be enrolled in the study if they, or their next of kin, have given their consent.

As part of this study so far, DNA samples have been collected from almost 2,000 patients.

Chris Wigley, CEO of Genomics England said: “At Genomics England, we are extremely proud to be working with the NHS and other partners in the fight against COVID-19, to understand why people respond differently to this infection.

“Our goal with this study is to help the national response to this terrible pandemic, using the experience we have gained through the 100,000 Genomes Project, and leveraging our ongoing work in genomic research and healthcare. As with all groundbreaking science, we don’t know what the answer is yet – but we are convening the finest minds in academia and industry to try to find out.”

Genomics England will read the data from entire genomes – or genetic blueprints – of thousands of people who have been most severely affected by coronavirus and compare them to those who experience only mild symptoms.

Dr Kenneth Baillie, Chief Investigator at the University of Edinburgh, leading this study, said: “Our genes play a role in determining who becomes desperately sick with infections like COVID-19. Understanding these genes will help us to choose treatments for clinical trials. The GenOMICC study was launched before this outbreak and it is recruiting in more than 160 ICUs across the country with tremendous support from the critical care community. We are excited to work with Genomics England to tackle this new and complex disease.”

By combining the genome with rich clinical characteristics and comparing those who become severely ill with those that experience a much milder illness, the consortium hopes to gain new insights into how the virus affects us.

This ground-breaking research may help explain why some patients with coronavirus experience a mild infection, others require intensive care and why some patients die from the disease.

By discovering why some people are predisposed to developing life-threatening symptoms, the consortium will be able to identify treatments which have the best chance of success in clinical trials, and potentially identify people at extreme risk if they develop COVID-19.

This work – sequencing human genomes – complements the UK COVID-19 Viral Sequencing Programme (COG-UK) announced in March and its work already underway to sequence the genome of the virus itself, led by Public Health England and the Sanger Institute.

Professor Sir Mark Caulfield, Chief Scientist at Genomics England, said: “For the first time in a generation we face a global viral pandemic that is life threatening for some people, yet others have a mild infection. By reading the whole genome we may be able to identify variation that affects response to COVID-19 and discover new therapies that could reduce harm, save lives and even prevent future outbreaks.”

Whole genome sequencing will be carried out by Illumina at its laboratories in Cambridge, UK, where they successfully delivered the 100,000 Genomes Project together with Genomics England and the NHS.

Paula Dowdy, General Manager and SVP Illumina, EMEA, said: “We have a long-standing partnership with Genomics England and are proud to support this new genomics initiative from our Cambridge-based lab. The results will establish a unique platform for researchers to understand the human response to coronavirus infection, leading towards new treatments and ways to control infection spread.”

Today’s announcement demonstrates how different parts of the UK’s world-leading genomics community are working together to get a full picture of both the spread and impact of the virus.

Data from the person’s own genome can be linked to the virus genome data provided via the previously announced viral sequencing programme by the COVID-19 Genomics UK Consortium (COG-UK), a partnership of NHS organisations, UK public health agencies, the Sanger Institute and UK academic centres.

Professor Sharon Peacock CBE, Director of COG-UK, said: “This study is a fantastic example of how different parts of the UK genomics community are working together to get a full genomic picture of the spread and impact of the virus. In COG-UK we have already sequenced over 10,000 virus genomes from patients with COVID-19. Linking this data to the patient’s own genome data in the Genomics England-GenOMICC study may provide unique insights into how the patient and virus genomes act together to influence the patient’s response to the infection and will help inform and improve our response to future outbreaks.”

Professor Sir Mark Walport, Chief Executive of UK Research and Innovation (UKRI), who have given £3 million in funding to the project, said: “The UK is a global leader in the genetic analysis of disease. By applying this expertise to examine the role of genetic factors in COVID-19, including in young severely impacted patients without known underlying health issues, this study could identify important risk factors and disease mechanisms, which may lead to new diagnostic and therapeutic approaches.”

Part of the overall genomic study will also focus on children and young adults severely affected by COVID-19.

The NIHR BioResource is partnering with GenOMICC and Genomics England to provide infrastructure, expertise and £1 million funding to investigate this by collecting samples from these young patients and their parents.

Professor John Bradley CBE, Chief Investigator of the NIHR BioResource, said: “The NIHR BioResource is delighted to build on our established partnership with Genomics England and work with GenOMICC to understand in particular why some children and young adults are so severely affected by COVID19.”

These initiatives will enable novel insights into the virus, as well as possible human factors that influence the effects of the disease, and whether a combination of both shape outcomes for NHS patients.

Professor Dame Sue Hill, Chief Scientific Officer and SRO for Genomics at NHS England and NHS Improvement said: “This study has the potential to dramatically improve our understanding of COVID-19 – it could help us to identify whether underlying genomic differences play a part in how people react to the virus and why some people have few or no symptoms whilst others can get very ill.  I am very grateful to all the staff, patients and families who are working on and participating in this study, at what is a very challenging time.”

The data that is collected during the study will also inform global strategic planning for possible later waves of the pandemic, and for new pandemics in the future.  For now, the prospect of this study’s findings should not detract from the fact that we must all continue to follow the government’s guidance, which at the moment involves staying home and staying safe.

  • Since genetic discoveries need very large numbers of patients, patients who have already had COVID-19 and have now recovered are invited to volunteer to take part in the study. To register your interest, please visit www.genomicsengland.co.uk/covid-19/

Baroness Blackwood appointed Chair of Genomics England

Baroness Nicola Blackwood has been appointed Chair of Genomics England, succeeding Baroness Dido Harding, who has served as Interim Chair since November 2019.

Genomics England was established in 2013 to deliver the 100,000 Genomes Project in partnership with the NHS and helped to cement the UK’s world-leading position in genomic science.  Following the successful sequencing of 100,000 whole genomes in December 2018, Baroness Blackwood will support Genomics England through its next phase of development, which will see it move from a project-based organisation to a sustainable government-owned company, with a mission to facilitate and expediate genomic research, and accelerate the transition to genomic healthcare.

Baroness Blackwood was a Parliamentary Under Secretary of State at the Department of Health and Social Care from January 2019 to February 2020 and previously served as Parliamentary Under Secretary of State at the Department of Health from July 2016 until June 2017. She was elected as the Conservative MP for Oxford West and Abingdon in May 2010.

Health and Social Care Secretary Matt Hancock said:

It’s a great pleasure to welcome Baroness Blackwood as the new Chair of Genomics England. Nicola brings huge experience to the role, including from her time as Life Sciences Minister, and I’m certain she will drive forward the crucial work already underway to better our understanding of the human code and the health benefits that can bring. I thank Baroness Dido Harding for the significant contribution she made to Genomics England, helping to spearhead the organisation as a world leader in genomic science.

 Baroness Blackwood of North Oxford, Chair of Genomics England, said:

I’m thrilled to accept the honour of becoming Genomics England’s Chair. This is a tremendously important time to be able to contribute to Life Sciences in this country. I truly believe that genomics will continue to transform healthcare, allowing us to build a sustainable healthcare system, delivering personalised and predictive care to everybody. I’m absolutely committed to supporting Genomics England as best I can, through the fight against COVID-19 and beyond.

 Chris Wigley, Chief Executive Officer of Genomics England, said:

I’m delighted to welcome Nicola to Genomics England.  Her wealth of experience in the public and private sectors – particularly her past role of Life Sciences Minister – will be invaluable to the Board, our many partners, participants, and all of our staff, as we strive to facilitate genomic research and to make genomic healthcare universally accessible. I am confident that, with Nicola’s support and guidance, Genomics England will play an ever-more significant role in the UK’s genomic healthcare ambition.

On behalf of the Board, I would like to thank Dido for her outstanding contribution as Interim Chair of Genomics England. We have been extremely fortunate to have benefitted from her deep knowledge and broad expertise in leading the Genomics England Board.

Professor Sir Mark Caulfield at QMUL’s Precision Medicine Leadership Event

On 5 March 2020, Professor Sir Mark Caulfield, Chief Scientist at Genomics England, delivered the keynote talk at St Bartholomew’s Great Hall for the Precision Medicine Leadership event co-hosted by Queen Mary University London (QMUL).

The event set out to explore how collaboration can enable and advance precision medicine, showcasing new developments in the field from academia and industry. The event fostered networking opportunities between delegates who attended from more than 30 companies spanning pharma, biotech, data analytics, intellectual property law, medical writing, funding bodies and life sciences consulting.

Professor Sir Mark Caulfield gave insights into the growing importance of precision medicine in the UK, and detailed Genomics England’s contribution towards this, including:

  • the ground-breaking 100,000 Genomes Project
  • collaboration on the NHS Genomic Medicine Service
  • Enabling the UK Government’s Life Sciences ambition of sequencing 5 million genomes in 5 years.

Professor Sir Mark Caulfield spoke alongside Professor Claude Chelala of Bart’s Cancer Institute and Professor David van Heel of the QMUL Blizard Institute. Industry talks were given by AstraZeneca, precisionlife, Celyad, Cerba Research and Roche. The event concluded with a dynamic panel discussion involving Professor Rakesh Uppal of Bart’s Life Sciences and Jane Theaker, CEO at Kinomica Ltd., a spin out company of QMUL.

You can watch a summary video of the event here (external link to LinkedIn).

Genomics England’s response to COVID-19

At Genomics England, we continue to carefully monitor the coronavirus (COVID-19) situation as it rapidly evolves. Our immediate priorities are to protect and support the health and well-being of our staff, and the professional and social communities with whom we work, whilst continuing to work with our partners at NHS England, as well as those in government, industry, medicine and academia, to accelerate genomic research and healthcare.

In response to government advice, we are working proactively to reduce the spread of the virus. On Tuesday 17th March 2020, we asked all of our staff to work remotely. Our offices are now all closed, with the exception of Dawson Hall, which remains accessible for the time being for urgent issues, such as IT hardware services or essential small meetings. We are enormously proud of our staff, who have adapted incredibly quickly to this new way of working, using technology such as Microsoft Teams and Slack to keep in touch, and finding innovative ways to keep in touch such as ‘virtual coffee breaks’ and ‘walk and talk’ sessions (combining some fresh air with a daily team call). Everybody’s positive attitude and determination has been truly inspiring.

We are very proud to be playing an important role in the ecosystem that is responding to the immediate threat. Some of our team are likely to be called back to front-line care within the NHS, and others are supporting research efforts to reduce, and hopefully eliminate, the risks that COVID-19 is currently presenting. This virus clearly poses additional risks to many of the people who we are striving to help, not only in terms of physical health, but also as a result of reduced access to care, or isolation. We are committed to doing everything that we can to support our participants, and those who are receiving care through the NHS Genomic Medicine Service. We will be exploring new and innovative ways to support these communities during these challenging times.

People remain at the centre of everything that we do, and that includes our response to COVID-19. Our thoughts are with everybody who has been affected by this outbreak – patients and their loved ones – and also, the many thousands of remarkable people who are selflessly working around the clock, on the front-line of healthcare, government and research, to support patients and bring the pandemic under control.

At Genomics England, we take our responsibility to the communities we serve very seriously and will continue to do all we can to contribute to the national and international efforts to support those who most need our help.

Rare Disease Day 2020 – diagnosis is just the start of another journey for patients

Today is Rare Disease Day 2020. The 100,000 Genomes Project is coming towards an end as we have finished sequencing everyone’s genomic samples, and are working hard to get the last few reports back to the NHS. To mark and raise awareness for the occasion, we asked Dr Christine Patch, Clinical Lead for Genetic Counselling at Genomics England, to give us her perspective.

Professor Christine Patch, Clinical Lead for Genetic Counselling

Projects such as the 100,000 Genomes Project and others are directly facilitating new genetic diagnoses for patients with rare disease. The research that will happen as scientists explore this genomic information will lead to greater understandings of rare disease and create the possibility of new treatments. In the short to medium term, as health services such as the NHS in England implement new technologies and make access to appropriate genetic testing easier and more efficient, the excitement and hope is that many more patients and families with rare diseases will be able to avoid the long diagnostic odyssey and get a diagnosis and explanation more quickly.

In the optimism and excitement about this however, we must not forget that the diagnosis is just the

start of another phase of the patient and family journey. We know that rare disease charities and advocacy groups are already asking the question – what happens next? Projects like the 100,000 Genomes Project, and its collaboration with the NHS and the participants, has made real progress, but it is also just the start.

As a health professional I think our obligations to patients and families with rare disease includes thinking about how we can impact on the next stage, and use our resources to focus on how we work with and support patients and families to manage the impact of genetic information in their lives, which for some will include the impact for future generations.

Participants in 100,000 Genomes Project instrumental in ground-breaking advance in understanding of bowel cancer growth

Genomic data provided by participants in the 100,000 Genomes Project has helped Cancer Research UK researchers identify how a common type of gut bacteria could contribute to bowel cancer.

The research, undertaken by a team of international researchers led by Professor Hans Clevers in the Netherlands, shows that a toxin called colibactin released by a strain of E. coli, causes unique patterns of DNA damage to the cells lining the gut. These ‘fingerprints’ were also seen in bowel cancer tumours, showing a direct link between the bacterial toxin and the genetic changes that drive cancer development for the first time.  This work demonstrates the value of Cancer Research UK’s Grand Challenge to understand how bacteria may influence cancer.

Sequencing data for the paper was provided by Genomics England from participants in the 100,000 Genomes Project and is published in Nature today. Working with scientists including Dr Henry Wood and Professor Philip Quirke FMedSci from the School of Medicine at the University of Leeds, Genomics England provided 2,208 genomes for the project, without which the findings would not have been demonstrable.

Ian Hartley, a participant in the 100,000 Genomes Project who donated his genomic information for the project during receiving cancer treatment, said:

I’m thrilled that my cancer experience, however negative it was at the time, has helped in a small way deliver such a positive leap forward in our understanding of how bowel cancer develops.

I was approached about the 100,000 Genomes Project by my doctors early on in my treatment to see whether I wanted to volunteer. For me, it was a no-brainer to say yes. Providing researchers with genomic information has so much potential to help not only the individual with treatment and early diagnosis, but also all of us collectively. These findings demonstrate that in the clearest terms.

I would strongly encourage anyone who is unsure about whether to donate their data to do so. The more open we are about the advantages of genomic research, the better. The bigger the genomic data bank Genomics England has, the more advances like these can be made.

As well as identifying for the first time a toxin as a probable new cause of bowel cancer, the research team has suggested that detecting this specific DNA damage in the cells lining the gut could one day allow doctors to identify people at higher risk of the disease and be used alongside current bowel cancer screening tests.

Commenting on the findings, Professor Sir Mark Caulfield FMedSci, Chief Scientist at Genomics England, said:

Genomics England are delighted that data provided to us by our participants from the NHS has enabled researchers to help accelerate these findings, which are a world-first. Without the participation and generosity of Ian and all the others, this outcome would not have been achievable.

There are around 42,000 new bowel cancer cases in the UK every year, and it remains the second most common cause of cancer death. These findings enabled by the UK’s 100,000 Genomes Project opens a new vista on the biology of colon cancer and has significantly improved our understanding of how this type of cancer develops. We are very optimistic that this research will ultimately lead to improved diagnoses and better outcomes for patients.

Our participants, who contribute to the continual growth of our research environment and the quality of the data within it, are critical in facilitating the genomic research that leads to clinical insights like these which are leading the world.

Genomics England and Illumina partner to deliver whole genome sequencing for England’s NHS Genomic Medicine Service

Genomics England and Illumina today announced a new agreement to deliver up to 300,000 whole genome equivalents over the next five years, with an option to increase to 500,000. Samples will be provided through the NHS Genomic Medicine Service and the network of seven genomic laboratory hubs across England, which were established in 2018. This supports NHS England’s ambition to lead the world in introducing whole genome sequencing into routine healthcare. Samples will also be provided by Genomics England and from the Government’s Life Sciences Strategy for research purposes.

The agreement builds on the successful delivery of the 100,000 Genomes Project (100KGP), which established consent from patients with rare genetic diseases and cancer, tissue sample requirements, standardised DNA sequencing, data analysis and reporting.  It also supports the ambition described by the Rt. Hon. Matt Hancock, Secretary of State for Health and Social Care, to analyse up to 5 million genomes (including whole genome sequencing) by 2024, enabling the UK to maintain its position as a global leader in genomics.

Under the agreement, and guided by the National Genomic Test Directory, samples from NHS patients in England with known rare diseases and cancer types will be eligible for whole genome sequencing, to support diagnosis, inform and improve treatment pathways, and ultimately improve outcomes. The expectation is that the number of eligible clinical indications will expand over time.

The agreement will also continue to facilitate translational research programmes begun by NHS England and Genomics England during the 100KGP with a view to improving patient outcomes through enhanced genomic diagnostic insights.

Whole genome sequencing will be performed by Illumina Laboratory Services (ILS) in Cambridge, UK, operating under Medical Laboratory accreditation (ISO 15189) using the NovaSeq 6000, BaseSpace Sequence Hub and Illumina analysis tools.

Professor Dame Sue Hill, Chief Scientific Officer for NHS England said:

The introduction of whole genome sequencing as part of routine clinical care, as signalled in the NHS Long Term Plan, represents a step change in the genomic testing available on the NHS as part of the Genomic Medicine Servi as part of our world leading offer to patients. This will enhance our ability to fully embrace all aspects of personalised medicine from predictive prevention to a more precise diagnosis and targeted treatment for better outcomes.

Nicola Blackwood, Health Minister said:

Genomic medicine has enormous potential to improve the diagnosis and treatment of some of our deadliest diseases – helping patients to live longer, healthier lives. Our 100,000 Genomes Project has already delivered life-changing results for many people, and this agreement between Genomics England and Illumina is another transformative step towards the NHS becoming a truly predictive, preventative and personalised health service.

 

Professor Sir Mark Caulfield, Chief Scientific Officer of Genomics England said:

Delivering 100,000 genomes was a tremendous achievement, which would not have been possible without the partnership of the NHS, and the academic, clinical and commercial communities. We are delighted to be extending our relationship with Illumina, who have been an invaluable partner since 2014, and continue supporting the accelerated uptake of advanced genomic medicine into the NHS. The UK is already leading the way, but this agreement builds on the strong foundations by demonstrating further the commitment of the UK life sciences sector to supporting the NHS’ delivery of truly personalised care.

Dr David Bentley, Chief Scientist, Illumina said:

Building on the highly innovative and successful 100,000 Genomes Project, we’re delighted to move to the next phase of working with Genomics England, and now also with the NHS, to help transform England’s healthcare service into the first in the world to benefit from routine whole genome sequencing. The research component of this agreement is also incredibly important as, together, we will develop new approaches to unlocking the power of the genome and go on to identify more variants that underpin the full panoply of human diseases.

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