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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.

New Year Honours for Genomics England Board members, Jonathan Symonds CBE and Professor Dame Sally Davies DBE

Genomics England’s former Chairman, Jon Symonds CBE, has been Knighted for services to UK Life Sciences and Finance. Jon brought tremendous leadership, insight and direction to Genomics England during his tenure as Chairman, and his firm belief in the potential for genomic science to transform the way in which healthcare is delivered has been critical in driving our vision. We are very fortunate to have Jon’s continuing insights and direction as he continues to serve on the Board, and are delighted that his service has been recognised in this way.

Professor Dame Sally Davies DBE has also been further recognised, with the Dame Grand Cross of the Order of the Bath, for her services to Public Health and Research. Her experience and broad knowledge continue to be invaluable in her capacity on our Board and we are tremendously grateful for her guidance and support.

We offer them both our warmest congratulations for this very well deserved recognition.

Australian Genomics launches local instance of PanelApp

The sharing of information about gene-disease associations between Australian laboratories will be made far easier from today as Australian Genomics launches a local instance of PanelApp.

PanelApp was designed by Genomics England for the 100,000 Genomes Project, and now the platform is being used to reach a consensus in gene panel content for genetic tests in the NHS Genomic Medicine Service. The Genomics England team have made the platform, which does not store identifiable clinical data, open source and have worked closely with Australian Genomics to establish an Australian node of the platform.

The open nature of PanelApp allows the crowdsourcing of contributions from many experts, facilitating timely identification of newly published evidence regarding gene-disease associations.

PanelApp allows diagnostic laboratories, clinicians and researchers to:

  • share structured gene-disease validity assessments;
  • create and compare evidence-based virtual gene panels for genomic analysis;
  • contribute towards national and international efforts to establish consensus gene-disease relationships.

Ellen McDonagh, Head of Curation at Genomics England, said:

We’ve created this platform to enable worldwide crowdsourcing of expertise and curation of consolidated knowledge. The aim is to reach consensus on gene-disease relationships, and we have successfully used the platform for the 100,000 Genomes Project and now nationally to support the NHS Genomic Medicine Service, This will help deliver best practice in genomic analysis.

“We’re delighted our colleagues in Australia have picked up PanelApp and are adapting it to their needs,” said Augusto Rendon, Chief Bioinformatician at Genomics England.

“This has been made possible through the partnerships that Australian Genomics and Genomics England have built as Driver Projects under the Global Alliance for Genomics and Health – demonstrating the benefits of sharing tools, knowledge and expertise globally.”

Currently in Australia, the process for documenting and sharing gene-disease associations is manual and inefficient. The consolidation of multiple disparate silos of activity into a single open national platform will reduce the gene curation burden on individual laboratory and clinical services and improve diagnostic outcomes for Australian patients.

“PanelApp Australia marks a huge step forward in enabling more efficient and robust diagnostic practices in Australia. I encourage local laboratories, clinicians and researchers to sign on to the platform and lend their expertise,” said Associate Professor Zornitza Stark from Australian Genomics, who coordinates content management for the platform.

PanelApp Australia already contains virtual panels designed and used by Australian Genomics Flagship projects, Melbourne Genomics Flagships, the KidGen Collaborative, Victorian Clinical Genetics Services, Genetic Health Queensland and The University of Melbourne’s Centre for Cancer Research (UMCCR).

Associate Professor Oliver Hofmann’s Genomics Platform Group team at UMCCR have been responsible for the technical deployment of the Australian instance of PanelApp.

“We hope to continue to co-develop the platform in the future, connecting the two instances to facilitate knowledge transfer between Genomics England and Australian Genomics, as well as extending PanelApp Australia for somatic use case,” said Associate Professor Hofmann.

PanelApp Australia is now live and available at panelapp.agha.umccr.org

Any questions and queries can be directed to panelapp@australiangenomics.org.au.

Follow the Genomics England PanelApp Team on Twitter @PanelAppTeam
Follow news from the Australian Genomics PanelApp Team: @PanelAppAus
Follow GA4GH: @GA4GH

Dido Harding to become new interim Chair of Board

Photo credit: NHS Improvement

Baroness Diana ‘Dido’ Harding is to become interim Chair of the Genomics England Board, starting from December 2019, as Jonathan Symonds CBE steps down at the end of November. Our CEO, Chris Wigley, says a few words below.

Jon Symonds will be stepping down as Chair of Genomics England, with effect from the end of November. Jon’s new role as Chairman of GSK means he is not able to continue as our Chair, but we are delighted that he will be staying on as a Board member.

We are very pleased to announce that Dido Harding has accepted the role of Chair of Genomics England on an interim basis. We anticipate that Dido will act in this role for at least six months, whilst we complete our search for a permanent Chair.

On behalf of the Board, our many partners and all of our staff, I would like to thank Jon for his outstanding contribution as Chair of Genomics England. We look forward to our continuing relationship with Jon, both in his ongoing capacity on our Board, and also as he begins a new role as Chairman of GSK. We will continue to build on our shared commitment to delivering sustainable, personalised medicine and improving the lives of populations across the world.

Dido brings a wealth of experience and expertise from both the private and public sectors. Her breadth of knowledge and experience will be invaluable to Genomics England as we broaden our vision and begin our next chapter. Dido is currently Chair of NHS Improvement, the body responsible for overseeing and supporting NHS providers and trusts in England. She also sits in the House of Lords as a Conservative peer and is a member of the Economic Affairs Select Committee. Prior to this she was Chief Executive of TalkTalk Telecom Group plc, between 2010 and 2017.

I firmly believe that with Dido’s support, the exceptional team here, working in partnership with the NHS and many others, will continue to drive a global transformation in healthcare.

National Conversation on Rare Diseases survey

In July, the Minister for rare disease at the Department for Health and Social Care, Baroness Blackwood, announced a ‘national conversation’ on rare disease. This conversation aims to gather a range of views from the rare disease community to identify common themes which will then feed into an overarching framework to follow the UK Strategy on Rare Diseases, which runs until the end of 2020.

To start the conversation, the Department of Health and Social Care have developed surveys to collect views from the patient community, healthcare professionals, researchers and industry, to understand the major barriers the rare disease community are facing. These surveys were developed with the help of stakeholders and will be used by government to inform a rare disease framework to improve the lives of people living with rare diseases.

In the survey, you will be asked about your background as a member of the rare disease community (e.g. the nature of your condition or your work on rare diseases) and what you think are the greatest challenges faced by those living with, caring for, or developing treatments for rare diseases.

Survey responses will be used exclusively for the national conversation on rare diseases and related policy work by the rare disease policy teams across the UK Government departments. It will not be shared with any third parties. Responses will be anonymous unless you choose to share your personal details such as your name and email address.

Follow this link to find out more and take the survey – the deadline for responses is Friday 29 November.

Please note that everyone filling out the survey will use the same link. You will be asked which group you belong to as part of the survey.

Genomics England is key partner in two HDRUK Digital Innovation Hubs

Today, Health Data Research UK (HDRUK) announced that seven data hubs are to be set up across the UK to speed up research for new medicines and treatments. This initiative will support quicker diagnoses, with the potential to save lives. The hubs will focus on curated, disease-focused datasets, clinical trials, and real world evidence. Genomics England is a key partner in two of these hubs: DATA-CAN and Discover-NOW.

DATA-CAN: Using cutting-edge research and innovation to benefit UK patients

DATA-CAN – the Health Data Research UK Hub for Cancer – aims to transform how cancer data from across the UK can be used to improve patient care. The hub will work with patients to bring their clinical data together and use this data to help develop improved cancer treatments, give patients faster access to clinical trials, and understand how we can improve NHS cancer services. The hub, hosted by UCLPartners, will be supported by patients, charities, clinicians, academic and industry-based researchers and innovators, and will involve cancer hospitals across the country. Other partners include Queen’s University Belfast, University of Leeds and Leeds Teaching Hospitals, and IQVIA.

DATA-CAN Director Dr Charlie Davie of UCLPartners said:

Working across all four nations of the United Kingdom, DATA-CAN is a unique partnership of NHS organisations, patients, charities, academia and industry working together to improve cancer care by harnessing anonymous clinical and genetic data to provide cancer patients with faster access to clinical trials, and to enable the development of new and improved medicines and treatment approaches.

The Hub will help us to provide the highest quality data allowing transformative change in cancer care

Jacqui Gath, cancer survivor and patient advocate (ICPV/YHCRP), said:

Patients want their data to be used to improve care. In fact they’re often surprised it’s not used already.

The work of the Hub and the new research it engenders will bring hope to the people who are diagnosed every year with this awful disease. One in two people will get cancer in their lifetimes and this Hub offers the hope and opportunity of saving 30,000 lives a year.

More information about DATA-CAN can be found here.

Discover-NOW: Using real world data to improve understanding of many long-term conditions

Discover-NOW is the Health Data Research Hub for Real World Evidence.  It is a unique partnership, led by Imperial College Health Partners, bringing together NHS organisations, globally recognised academic, technology, industry and charity partners as well as patients and the public to revolutionise the way health information is used to treat and prevent disease in the future.

Historically, health research has predominantly used data to look retrospectively. Through safe and secure curation of patient information, Discover-NOW will provide leading clinicians, researchers and scientists with access to de-identified linked patient information at scale in near to real time. This will enable them to look prospectively to identify new patterns in disease thus helping us to better manage many conditions and, in some cases, prevent them happening in the first place.

Discover-NOW Director Dr Axel Heitmueller said:

Through the safe and secure curation of patient information Discover-NOW will create a step change in the way health information is accessed and analysed to accelerate the development of new treatments, devices and applications that support better management and prevention of a range of conditions. This work will benefit millions of people into the future and contribute significantly to the health and wellbeing of our population.

John Norton, Citizen Partner of Discover-NOW said:

As a London citizen I am hugely excited about this initiative and the benefits it will bring to patients and the public. Through bringing information that already exists about us as patients together and enabling researchers and scientists to access this in new and secure ways, the Discover-NOW Hub could be the key to unlocking new life saving treatments or even preventing killer diseases altogether. Data really can save lives.

Find out more about Discover-NOW here.

Genomics England’s Chief Commercial Officer Joanne Hackett said:

We are delighted to be part of these two important Digital Innovation Hubs. We have a unique opportunity in this country to unite across healthcare, industry and academia using our expertise in genomic data. This is an important demonstration of the UK’s commitment to lead on innovative and practical approaches, to improve research and patient outcomes. We look forward to collaborating with our partners on this important work.

The Health Data Research Hubs are part of a four-year £37million investment from the Government Industrial Strategy Challenge Fund (ISCF), led by UK Research and Innovation, to create a UK-wide system for the safe and responsible use of health-related data on a large scale.

How can we make cancer treatment less toxic?

The answer is in your genetic code

Initial findings from a pilot study using 100,000 Genomes Project data may help doctors to decide which dose of medications are the most appropriate for different cancer patients to take.

Medicines can affect people in different ways – a drug might work really well in some people, but not work or even cause serious side effects (‘adverse reactions’) in others. Genetic differences between people are behind some of these different reactions to drugs. The study of these genetic differences is called ‘pharmacogenomics’. Knowing about pharmacogenomics can be very important in deciding which medications a patient should take.

The DPYD gene controls the process that breaks down many medicines in the liver so that they can then be safely excreted by the body. There is strong evidence that four variants in the DYPD gene increase the risk that a patient will suffer severe or fatal toxic side effects when treated with a type of drug called fluoropyrimidines. These drugs are commonly prescribed to patients with breast or colorectal cancer and include capecitabine or 5-Fluorouracil.

If a patient has one of these four variants of DPYD, these drugs are not broken down as well allowing them to build up to toxic levels in the liver. Published guidelines suggest that patients with these genetic variants should receive reduced doses of capecitabine or 5-Fluorouracil, or avoid the drugs completely in order to prevent toxic side effects. However this is not yet routinely done.

As part of the pilot, whole genome sequence (WGS) data from all cancer participants within the Project is now being analysed for the presence of these four DPYD gene variants. The findings are then being made available to Genomic Medicine Centres. If clinicians know that a patient has one or more copies of one of these variants, they will be able to assess whether adjusting therapy regimens may reduce the risk of toxicity. Feedback on the action taken by the clinician will be recorded and analysed to help determine the clinical effectiveness of analysing these variants within the NHS. This demonstrates how whole genome sequencing can be used to ensure that patients get the most effective and least toxic medicines for their cancer.

  • Find out more about the variants being assessed in the cancer analysis technical document here.
  • There is NHSE published guidance for clinicians on validation and reporting of DPYD variants available here.
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