Category: Genomics England

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.

Over 100,000 whole genome sequences now available for approved researchers

Data Release 7 has now gone live in Genomic England’s Research Environment. While every data release is significant in its own right, v.7 is symbolic. It means we have now passed the milestone of 100,000 whole genomes available to researchers. Of course it’s not just about genomes. The growing wealth of linked clinical and secondary health data associated with the genomic data in each release is what makes the Genomics England dataset one of the most exciting tools in the world for discovery and translational research.

Speaking on the importance of this release, Genomics England Chair Jon Symonds CBE, said:

The completion of the sequencing of the 100,000 Genomes Project in December was a major accomplishment, representing a tremendous effort across Genomics England and the NHS. Today, we are proud to announce that over 100,000 genomes are now available to researchers through our secure Research Environment. While our priority remains the return of results to participants, this milestone is representative of our commitment to improving patient outcomes through research. By generously consenting to allow their data to be used for research, participants are ensuring that future generations will benefit from the resulting healthcare technologies and treatments that will be made possible by the Genomics England research dataset.

Improvement of patient outcomes through precision medicine technologies is a long-term goal but in fact, researchers accessing the Genomic England Research Environment have already created impact for project participants. To date, there have been 94 researcher-identified potential diagnoses in addition to over 90,000 results returned to the NHS by the team at Genomics England.

Commenting on the research opportunity, interim Chief Executive Professor Sir Mark Caulfield, commented:

Through the Genomics England Clinical Interpretation Partnership and Discovery Forum, great progress is being made in understanding how this dataset can be used to advance scientific discovery and the development of new technologies. Genomics, and improving healthcare, is a global endeavour. As such we are proud to see public and private researchers from around the world recognising the opportunity our Research Environment presents. Their work helps us fulfil our commitment to project participants who want to see their data used to benefit patients globally.

To tell the story behind the numbers, we put a few questions to Dr James Holman, Research Environment Project Lead.

Dr James Holman

What is the significance of this data release and why?

It took a tremendous effort, across the NHS and Genomics England, to recruit thousands of participants and sequence over 100,000 genomes. Alongside that effort, Genomics England has been working hard to make those genomes available to researchers in our Research Environment. This release is a major milestone as it sees us exceed 100,000 genomes. It certainly hasn’t been a trivial exercise, and illustrates the commitment of Genomics England to accelerating scientific discovery. We owe particular thanks to the participants who have taken part in this endeavour.

It shouldn’t be forgotten that, although this one is symbolically significant, every data release has been important. Each release increases the richness of the linked clinical and secondary health data available to researchers, making our dataset a more powerful tool for discovery and translation. Similarly, following data releases will be just as important as we continue to enrich the Research Environment.

That being said, reaching 100,000 genomes in this data release is a significant achievement for the Genomics England Research Environment.

Can you provide a run through of what goes into a data releases and why they take time to prepare?

Each data release is a huge team effort across Genomics England. Together the teams collate, query, and generate data from numerous information systems across Genomics England and integrate them into a unified data release. These data are curated and made available in the various tools available within the Research Environment. That includes existing tools such as our Data Repository, and soon to be released applications such as the Data Discovery Portal and Genomics Analytics Platform.

Before the release goes live, we undertake an extensive review to confirm the integrity of the data and update the data dictionary. We then prepare a data release note to make users of the Genomics England Research Environment aware of what has been added or changed, making sure that we explain any new data features.

What’s coming up for the research environment for the rest of this year and what is your approach to development?

I am in the fortunate position of leading a team that is responsible for delivering innovative solutions to maximise the research potential of the data that’s available. In the coming months we will be delivering a range of new applications that will help researchers discover, understand, and use the data available within the Research Environment. We plan to deliver applications as advanced prototypes and then iteratively develop them based on user feedback. For each type of application released we are using surveys, pre- and post-release, to ensure the tools have the desired impact. This feedback will ensure that they meet the user needs and allow us to deliver value incrementally and continuously based on those needs.

Tools that we are currently testing and preparing for roll-out include a Data Discovery Portal, Terminology Service, OpenTargets, and a genomics analytics platform. We are also undertaking an evaluation of the common data model developed through the Observational Medical Outcomes Partnership (OMOP) Project to determine how suitable the model is for genomic analysis and what extensions may be required.

Chris Wigley appointed CEO of Genomics England

Genomics England has today announced the appointment of Chris Wigley as Chief Executive Officer, with effect from 1 October.

Chris joins Genomics England from QuantumBlack, a world leader in machine learning and artificial intelligence. Machine learning is critical in the analysis of the vast amounts of data involved in genomics, so Chris’ expertise in this area will be invaluable in driving Genomics England’s pioneering work with the NHS to realise the true potential of genomic medicine.

Chris was a Partner at McKinsey from 2009 to 2015. He then focused on growing QuantumBlack, a McKinsey company, as Chief Operating Officer. Prior to this, he worked with the British Foreign Office as a diplomat, and on digital transformation at the BBC.

The Chair of Genomics England, Jonathan Symonds CBE, said:

Chris joins us at a significant time for Genomics England as it takes the next steps in using the data entrusted to us by participants to transform healthcare.  Chris’ vision and energy will maintain Genomics England’s place as a world leader in genomic medicine. His leadership experience at QuantumBlack will be fundamental to our goal of building a world leading organisation delivering genomic science and analytics into routine medical care with our partners in the NHS and medical research.

Chris said:

I am tremendously excited to be joining Genomics England at this pivotal time. The fantastic work on the original 100,000 Genomes Project mission (which many thought was impossible just a few short years ago) shows the talent and grit in this team. Of course it would also have not been made possible without the cooperation of so many stakeholders and, most importantly, the participants who put their trust in the Project and to whom we are deeply committed.  Today, Genomics England’s partnership with the NHS is leading the world in bringing cutting-edge genomics research and analytics into daily medical care to benefit people across the UK and beyond. I can’t wait to join the team and help shape the next chapter in this extraordinary journey to bring digital technologies and products to clinicians and researchers and – most importantly – achieve transformative outcomes for patients.

Sir Mark Caulfield, who has acted as Interim CEO, will continue his excellent strategic scientific and clinical leadership as Chief Scientist in the next phase of transformation of genomic medicine in the NHS.

Jonathan Symonds said:

I would like to thank our Chief Scientist, Sir Mark Caulfield, who acted as interim CEO over the past six months. His leadership as Chief Scientist and commitment to delivering the 100,000 Genomes Project is respected around the world. Mark’s extraordinary contribution to genomics was recognised this year with a knighthood.

Matt Hancock, Secretary of State for Health and Social Care, said:

Genomics has huge potential to diagnose diseases earlier, unlock solutions for rare conditions and provide tailored treatments to individual patients to boost their chances of recovery. It could also help us drive the preventative agenda and help people avoid developing some diseases at all.

“We’re already leading the world in this exciting field and I’m delighted Chris will be helping us achieve our Long Term Plan ambition of bringing the benefits of personalised medicine to every patient, clinician and carer. Chris is a truly transformational leader and I have every confidence he will help the country realise our ambitious, world leading vision for Genomics England.

Baroness Blackwood, Parliamentary Under Secretary of State, said:

I want to personally congratulate Chris on his appointment as Chief Executive of Genomics England. He is an excellent leader with a proven track record of delivery, and I am very confident that Genomics England will go from strength to strength under his leadership. I want to also put on record my thanks to Sir Mark Caulfield for his work as interim CEO over the past six months. He has made a fantastic contribution to genomics over his career and I am very pleased that this was recognised with a knighthood in the Queen’s Birthday Honours.

Lord Prior, the chair of NHS England, said:

We are delighted that Chris Wigley will join Genomics England as Chief Executive. He has huge experience in digital innovation technological transformation and data analytics. His leadership and vision will bring exciting opportunities for Genomics England as it works hand in hand with the NHS to introduce personalised, precision medicines, early diagnostics and targeted prevention.

Q&A with Professor Sir Mark Caulfield

As you will have seen last weekend, we were delighted that our interim Chief Executive and Chief Scientist, Professor Mark Caulfield, was awarded a knighthood in the Queen’s Birthday Honours. We caught up with Sir Mark to hear his thoughts on receiving such an honour.

Congratulations Sir Mark! You must be very pleased to receive this honour – what does it mean to you?

This was not something I expected to happen ever, but I am so delighted that this recognition has come to Genomics England and myself. I do think this is a big testament to the entire team at Genomics England and our achievements. It is also humbling because I now know that a key factor in the award of this Honour was support from our Participant Panel.

How did you celebrate?

I celebrated on Saturday with my wife and my daughters with some champagne and a nice meal. As you are not supposed to tell anyone, the first big celebration was with the Genomics England team and then with the William Harvey Research Institute on Wednesday. I have been inundated by personal emails, cards and letters of congratulations.

This knighthood is recognition of a long and prestigious career, but are there any achievements that really stand out as highlights to you?

I think our team’s incredible dedication to delivery of the 100,000 Genomes Project and a new National Genomic Medicine Service stand out. I thank all of you for all you have done.

Is there anyone – scientist or otherwise – that has particularly inspired you throughout your career?

There are many but to name a few:

  • Professor Mike Floyer who was my Dean at medical school and was the most wonderful doctor who steadfastly supported me in my earlier career as a clinician, and was an inspirational role model who prized clear communication to patients and families.
  • Professor Rod Flower FRS who is a brilliant pharmacologist and has been a tremendous mentor throughout my career at the William Harvey.
  • Professor Sir Nick Wright and Dame Sally Davies who mentored me and gave me the opportunity of leadership.

What might your knighthood mean for Genomics England?

It signals public recognition at the highest level of our achievements as a team.

Do you think this honour will help to increase the awareness of genomics among the wider public?

It was great to be honoured alongside Prof Sir Peter Donnelly. To my mind much more important is the way we communicate genomics as a team and it is clear there is more to do here.

You’ve achieved so much already – what’s your next ambition?

To deliver a clear mission and delivery plan for the aspiration for 5 million genome analyses that commands the support of the Government and other funding.

 

Leading genomics expert awarded knighthood in the Queen’s birthday honours

Professor Mark Caulfield, the interim Chief Executive at Genomics England and Professor of Clinical Pharmacology at Queen Mary University of London, has been awarded a knighthood in the Queen’s Birthday Honours List.

Since 2013 Professor Caulfield has been instrumental in delivering the world-leading 100,000 Genomes Project, which hit its target of sequencing 100,000 whole genomes in 2018 and has already delivered life-changing results for patients.

This NHS transformation programme used whole genome sequencing to bring new diagnoses to people with rare diseases and to help choose cancer therapies.

To increase the value for participants in the project, Professor Caulfield established a coalition of 3,000 researchers worldwide and assisted the NHS in the creation of the National Genomic Test Directory. This will offer equitable access for 55 million people, depending on clinical need, to the appropriate genomic tests via a new National Genomic Medicine Service.

Professor Mark Caulfield said:

I have been incredibly lucky to stand amongst and alongside giants from our NHS, Genomics England, our universities, the government, our funders and most importantly, our participants. Together they helped me to transform genomics in healthcare. Their commitment, generosity, and trust has made our nation the world leader in the application of genomic medicine in the NHS. I am deeply honoured and thank every one of those who made this possible.

Jonathan Symonds CBE, the Chair of Genomics England said:

Mark’s knighthood is a fitting recognition of his pioneering and tireless work in genomics. He is an extraordinary clinician scientist whose contribution and leadership are respected worldwide for delivering the 100,000 Genomes Project. His role as Chief Scientist of Genomics England has seen whole genome sequencing reveal new diagnoses, improve treatments, and fuel medical research. It has benefited and will benefit many, many people across the world. This award is richly deserved.

Professor Colin Bailey, President and Principal of Queen Mary University of London, said:

I am delighted that Mark’s outstanding work in genomics has been recognised with such a prestigious honour. His pioneering work will pave the way for new diagnoses and precision healthcare across the globe. He is truly one of our stars at Queen Mary, and it is wonderful to see his contribution to science and medicine recognised with this honour.

Professor Caulfield graduated in Medicine from the London Hospital Medical College in 1984 and trained in Clinical Pharmacology at the Medical College of St Bartholomew’s Hospital and Queen Mary University of London, where he holds a Chair.

He has made substantial contributions to the discovery of genes related to cardiovascular health, cancer and rare diseases, including the discovery of more than 1,000 gene regions for blood pressure. He is amongst the top 1 per cent of the most highly cited researchers worldwide and his clinical pharmacology research has changed national and international guidance for high blood pressure.

Since 2000 he has been a Fellow of the Royal College of Physicians, and in 2002 he was appointed Director of the William Harvey Research Institute at Queen Mary University of London.

In 2008 he was elected a Fellow of the Academy of Medical Sciences, and became Director of the NIHR Barts Biomedical Research Centre.

Professor Caulfield was the academic lead for the creation of the Barts Heart Centre, bringing three hospitals together in 2015 to create the UK’s largest heart centre.

In 2013 he became an NIHR Senior Investigator and was appointed Chief Scientist for Genomics England where he has led the scientific strategy and delivery of the 100,000 Genomes Project, which sequenced the 100,000th genome on 5 December 2018. He became interim Chief Executive of Genomics England in January 2019.

The funders of this healthcare transformation leading to this award:

The 100,000 Genomes Project was primarily funded by the National Institute for Health Research (which also helped to recruit participants and store biological samples). Generous funding also came from the Wellcome Trust, the Medical Research Council, Cancer Research UK, the Department of Health and Social Care, NHS England, and the administrations of Scotland, Northern Ireland and Wales.

Matching mitochondria – Important new research uses 100,000 Genomes Project data

Professor Patrick Chinnery, Dr Ernest Turro, and Dr Wei Wei

Scientists publish new research using data from the 100,000 Genomes Project rare disease programme

Scientists from the University of Cambridge have announced a discovery about the inheritance of mitochondrial DNA using data from the 100,000 Genomes Project. The scientists are part of the neurology domain of the Genomics England Clinical Interpretation Partnership (GeCIP). These important scientific findings represent the beginning of a stream of valuable discoveries that will come from the 100,000 Genomes Project data.

The research has been published in the journal, Science. We asked study authors Professor Patrick Chinnery, Dr Ernest Turro, and Dr Wei Wei about their research. 

 

What do we mean by ‘mitochondrial DNA’?

Mitochondria, the ‘powerhouses’ inside cells that produce energy, have their own DNA called mitochondrial DNA. This is distinct from so-called ‘nuclear DNA’, which is contained in the cell’s nucleus and determines most of a person’s characteristics. Our nuclear DNA comes from both our mother and father, but our mitochondrial DNA only comes from our mother. Each cell can contain hundreds of mitochondria.

Nuclear DNA and mitochondrial DNA can change – these changes are called mutations. However, not all of the hundreds of mitochondria in a cell will have the same mutations. Having a mixture of normal and mutated mitochondrial DNA is called ‘heteroplasmy’.

Where did the data used in this study come from?

Our study was based on the analysis of nuclear and mitochondrial DNA in whole genome sequences from 53,300 individuals who were part of the National Institute for Health Research BioResource – Rare Diseases project, and the rare diseases programme of the 100,000 Genomes Project.

What did your study find?

In our study, we investigated how mitochondrial DNA mutations and heteroplasmies change when they are passed from a mother to her child. We found that 45% of people carry at least one mutation that affects more than 1% of their mitochondrial DNA. The proportion of mitochondrial DNA that carries a particular mutation can change when mitochondria are passed from mother to child. For some, the percentage level of heteroplasmy increases, and for others it decreases. This shapes mitochondrial DNA in the human population.

We also found that, for approximately 1 in 40 people in our UK-based study, their mitochondrial DNA originates from a different geographical population than their nuclear DNA. In these individuals, new mutations in their mitochondrial DNA are more likely to match the geographic origins of the nuclear DNA than the geographic origins of the mitochondrial DNA. This suggests that the nucleus is ‘shaping’ our mitochondrial DNA when it is passed from mother to child.

Do these findings have implications for patients or the public?

Although there are no immediate implications for patients or the public, our work gives the first clue that our cell nucleus ‘prefers’ some kinds of mitochondrial DNA. This might be important when carrying our ‘mitochondrial transfer’ to help prevent the inheritance of severe mitochondrial diseases.

Mitochondrial transfer is an in vitro fertilisation (IVF) technique for preventing inherited mitochondrial diseases. It involves taking the DNA out of a woman’s egg or embryo that has faulty mitochondria and transferring it to a donor egg or embryo with healthy mitochondria.

Matching both the mitochondrial background and the nuclear background of the donor could be important when selecting potential mitochondrial donors, although further work is needed to show whether this will be important in the long term.


Dr Freya Boardman-Pretty from the Genomics England Clinical Interpretation Partnership (GeCIP) team, explains how the GeCIP helps to enable important research like this to happen.

How does being involved with the GeCIP help scientists to carry out important research?

The GeCIP (Genomics England Clinical Interpretation Partnership) is a community of researchers and clinicians from academia and healthcare, who are based in the UK and worldwide. This community uses the 100,000 Genomes Project data to improve our understanding of genomics and health.

The Project dataset is an incredibly rich and unique resource. As well as the 100,000 whole genomes from participants, it also includes detailed clinical data such as linked longitudinal health records from the NHS. Access to this detailed and comprehensive information helps scientists and clinicians to answer questions about health that we have not been able to answer before.

How does the work of the GeCIP community help patients?

One important aim of the GeCIP is to use the community’s expertise to find diagnoses for the 100,000 Genomes Project participants where our interpretation pipeline has not found a possible cause of their disease. This means Genomics England can feedback additional diagnoses to individual patients and improve the way results are interpreted in the future.

GeCIP includes many diverse research areas, called “domains”. Scientists studying rare diseases often look for novel genes that might play a part in how a disease develops and progresses. Cancer researchers aim to identify new mutations that might promote the development of cancer, or use genetic and clinical data to study how cancers change when patients undergo treatments.

Identifying relevant genes in disease can open up new avenues of research, and help us to find new treatment options for patients.

The Science Advisory Committee and Access Review Committee assess each domain’s research aims before they begin their work. This also allows participants to review which questions and problems scientists are working on.

What does being a member of the GeCIP involve?

Members of the GeCIP apply to join wanting to answer specific questions, but we also expect them to contribute to wider knowledge across the Project, such as adding expert reviews to PanelApp or helping to train new GeCIP members.

One of the main principles of the GeCIP is that research should be collaborative rather than competitive. Ongoing research is registered so that other GeCIP members can find projects that they might like to work on with other scientists. Hopefully, this avoids duplicating research efforts and ultimately leads to better scientific results.

The GeCIP is constantly growing, with numerous applications to join every week. Individuals can apply to join here.

You can read more about this study on the University of Cambridge website

Genomic medicine will change the relationship between the NHS and the people who use it, according to a major new public dialogue project

The more widespread use of genomic medicine – applying knowledge about a person’s genetic information to guide and improve their healthcare – will change the relationship between the UK public and the NHS, according to a new report launched today. ‘A public dialogue on genomic medicine: time for a new social contract?’ explored public aspirations, concerns, and expectations about the development of genomic medicine in the UK. It was commissioned by Genomics England and co-funded by UK Research and Innovation’s Sciencewise programme in support of public dialogue on scientific and technological issues.

Led by Ipsos MORI’s Public Dialogue Centre, in-depth discussions between experts and members of the public across the country revealed widespread optimism about the potential of genomic medicine to improve our health and develop new and better treatments for disease and ill health. However, the report found that the delivery of genomic medicine will need widespread support and engagement from the public, clinicians, and researchers alike.

The dialogue reported that advances in genomic medicine may change public expectations around donating their data; and that clinicians and researchers will need to be equipped with ‘genomic literacy’ to support patients and donors and explain the ever-closer relationship between research and clinical care. The ways that medical charities, research organisations, and industry work with the NHS, and the importance of basic biological research, will also need to be better explained.

The NHS was founded on a common set of principles and values, as outlined in the NHS Constitution, that bind together patients, the public and NHS staff, helping the service work in an effective and equitable way. The new dialogue revealed that although participants were unfamiliar with the terminology around this ‘social contract’, they had very clear perceptions of how the NHS works and the ‘deal’ between the service and patients.

The report recommends that these advances from genomic medicine– particularly where they affect the core values of reciprocity, altruism, and solidarity (see notes below) – should be enshrined in the NHS Constitution.

The project also found that whilst there was widespread enthusiasm and support for genomic medicine, the public also have clear limits for how far they thought genomic data, and information derived from it, should be used. These red lines included genetic engineering, use of genomic data to differentiate groups within society, and for predictive insurance tests and targeted marketing. Participants wanted assurances that there is a robust governance framework and consent process in place that makes it clear what the intended use of their data is.

The Chief Medical Officer for England, Professor Dame Sally Davies, said: “I am delighted to see the publication of this important and timely report. It is increasingly clear that developments in genomics have the potential to significantly improve human health. Furthermore, the ability to provide the best care for patients can be greatly enhanced by comparing their data with that of many others. These benefits, which depend upon the safe collection, secure storage, and controlled use of patient information, are only fully achievable and sustainable in the context of well-founded public trust and confidence.”

Professor Michael Parker, Wellcome Centre for Ethics and Humanities, University of Oxford, said: “This report highlights the crucial role that ethics and participant engagement play in establishing and maintaining public trust in genomics. It is essential reading for everyone with an interest in genomic and data-driven medicine. It presents the results of an inclusive and thorough process of public dialogue and makes a vital contribution to ongoing discussions about genomic medicine. It reveals that the relationship between the NHS, patients, and the public is currently understood in terms of three core values: reciprocity, altruism, and solidarity. These values are likely to continue to inform the understanding of the appropriate relationship between medicine, research, and society as genomic medicine plays a more central role in healthcare.”

Professor Mark Caulfield, Chief Executive of Genomics England, said: “This dialogue is enormously important and timely as genomic medicine becomes mainstreamed in healthcare.  We need to support healthcare professionals as they work with patients to discuss the risks, benefits and other implications of genomic medicine with patients and the public. We need to describe clearly how genomic data will create a feedback loop that benefits both research and clinical care.  Building trust in this exciting and revolutionary area of medical science is absolutely essential to its success. Involving participants in all stages of our pioneering 100,000 Genomes Project was instrumental in putting a trusted system in place.”

Sarah Castell, Head of Futures at Ipsos MORI and the dialogue lead, said: “The members of the public at our events put a lot of work into this dialogue as they uncovered the ethical and practical dilemmas which the growth of genomics might bring. They questioned experts, explored case studies and examples, and developed their own views with great insight and flexibility of thought.  By the end of the sessions, participants expressed the same requirements from genomics as the public often asks of new technologies: they want genomics to bring clear benefits, to avoid unintended negative social consequences, and for those benefits to be shared fairly across all of society.”

Simon Burall, Programme Director for Sciencewise, said “Sciencewise has supported over 50 public dialogues on a wide range of scientific innovations. This project with Genomics England demonstrates why government departments invest in deliberative dialogue. By bringing together a diverse and inclusive sample of the public to engage deeply with the issues raised by the latest scientific advances, policy makers can get beyond the loud voices in the debate to gain insight into public perspectives. This helps them to understand how the public balances the trade-offs between the benefits that many of these innovations bring, and the societal harms that may also result, leading to better policy and a more trustworthy system of governance for the technology in question.”

Health Minister Nicola Blackwood said: “Genomic medicine has enormous potential to transform healthcare by diagnosing diseases earlier, personalising care to individual patients, and giving researchers the crucial information they need to develop cutting-edge treatments of the future. We are determined to embrace it through our Long Term Plan for the NHS. It is absolutely vital people have the confidence that their data will always be protected to the highest standards – and the Government has introduced tough new legislation to make this happen.”

 Download the report (PDF) here.



Notes:

The participants in the dialogue had very clear perceptions of why the NHS works. These were based on 3 concepts:

  • Reciprocity – the NHS will provide the best available care, in return for the public valuing that care
  • Altruism – the public want healthcare and research to benefit others as well as themselves
  • Solidarity – everyone pays their fair share and contributes individually to reducing the public health burden

Methods:

  • Ninety-seven members of the public, and thirty experts came to evening and reconvened day-long Saturday events, held in Coventry, Edinburgh, Leeds, and London.
  • A proportion of each group in each location was reconvened to a final Genomics summit event in London (n=23 in total), where the group was again joined by experts.
  • A total of forty-three experts attended the dialogue workshops and the Genomics summit.
  • A rapid light-touch literature review was conducted to inform the dialogue materials and to ensure that the project built on the work of previous social research on attitudes to genomics.   A stakeholder workshop including 19 participants also helped shape the framing of the dialogue, the materials and examples given to workshop participants.

The dialogue method involves in-depth discussion with relatively small groups of people; participant views are therefore not representative of the views of the wider public in the same way as a large scale survey. Nevertheless, the depth of discussion, time for reflection, scope of information provided, and interaction with experts, means that the views expressed here can be taken as a good indication of how an informed public might respond to complex ethical and practical questions around genomics.

Qatar Genome Programme and Genomics England formalise collaboration

Genomics England has signed a Memorandum of Understanding (MoU) with Qatar Genome Programme. The agreement lays the foundation for Qatar and the UK to develop a collaboration focusing on areas of research in genomics with global impact. The strategic research and development agreement aims to enable novel scientific discovery, and provide medical insights in genomics and precision medicine.

“This partnership aims to foster our shared goals for advancement of precision medicine and to facilitate common genomic research initiatives,” said Dr Richard O’Kennedy, Vice President for Research, Development, and Innovation at Qatar Foundation.

“Together we can push the boundaries further towards a new era of medical practice, where genomics can play a central role.”

Professor Mark Caulfield, Interim Chief Executive and Chief Scientist of Genomics England, said: “Genomics is a global, multi-stakeholder endeavour transforming healthcare. This collaboration will help expand the legacy of the 100,000 Genomes Project beyond the UK, and will allow us to better serve the diverse population of the UK. We are excited to share our expertise, and equally excited to learn from the approach of the Qatar Genome Programme.”

The MoU outlines a number of research activities between Qatar Genome Programme and Genomics England, such as establishing common frameworks to standardise genomic strategies for healthcare implementation; the evaluation of new technologies for whole genome sequencing; the cross-analysis of both national datasets; and the exchange of expertise related to educational programs. The two organisations will work together to share ideas, policies and regulations, technical expertise, and bioinformatics tools, and also to exchange staff, data and expertise in the field of genomics.

Commenting on the importance of the agreement, Professor Asmaa Al Thani, Board Vice-Chairperson of Qatar Biobank and Chairperson of the Qatar Genome Programme, said: “This agreement will see our two projects benefiting from a strategic alliance and the pooling of research talent and resources from both nations. The programme will also hopefully generate key industrial partnership opportunities enabling vital medical insights and breakthroughs.”

Attending the signing ceremony, His Excellency Mr Ajay Sharma, Her Majesty’s Ambassador to the State of Qatar, said: “I am delighted that the Qatar Genome Programme and Genomics England are signing this Memorandum of Understanding. The partnership between these leading institutions in genomic research will, I am sure, make an important contribution to tackling the healthcare challenges of today and tomorrow.

“This is another example of how the UK and Qatar are working together on Qatar National Vision 2030; and how this collaboration is of benefit to both our countries and others.”

Industry collaboration already benefiting participants of 100,000 Genomes Project

Alexion and BioMarin, both members of Genomics England’s Discovery Forum, have identified previously undiagnosed patients with life-threatening kidney and neurological diseases.

Diagnosing children likely to develop kidney failure

Nephronophthisis (NPHP) is a childhood genetic disorder primarily affecting the kidneys. It is rare (around 1 in 60,000 births) and usually results in kidney failure by the age of 15.  It is responsible for 15% of cases of childhood end-stage renal failure – with no preventative treatments currently available.

Using Genomics England’s dataset, global biopharmaceutical company, Alexion, has identified 14 undiagnosed patients, recruited as part of the 100,000 Genomes Project’s rare disease programme, who carry the gene deletion causing the disease. These findings have been shared with Genomics England and fed back to the patients’ NHS clinical teams.

“NPHP is a severe and devastating disease with significant unmet medical need. Our work with Genomics England has enabled us to identify previously undiagnosed NPHP patients, and it has helped us to understand the wide clinical spectrum that these patients show,” said Dr Guillermo Del Angel, Senior Director, Data Science, Genomics, and Bioinformatics at Alexion.

This discovery is an exciting first step in a broader collaboration between Alexion and Genomics England in applying data sciences and artificial intelligence across a spectrum of genomic and clinical data. The aim is to accelerate the diagnosis of patients suffering from rare diseases, enable paths of intervention, and bring hope to those with the disease and their families.

New hope for Batten Disease

Neuronal ceroid lipofuscinoses 2 (CLN2) is a very rare, inherited disorder caused by mutations in the TPP1 gene, and is one of a group of life-limiting conditions collectively known as Batten Disease. The symptoms typically emerge in children between the ages of two and four. CLN2 can lead to seizures, muscle twitches, vision loss, intellectual disability, and behavioural problems. Around 30-50 children live with the condition in the UK, and life expectancy is around 10 years. Currently, there is no cure or life-extending treatment for CLN2.

Biopharmaceutical company BioMarin, is another Discovery Forum member focused on rare disease patients.  It has identified one patient recruited into the 100,000 Genomes Project for a condition unrelated to CLN2, but who carries two pathogenic mutations of the TPP1 gene. This new information has also been fed back to the patient’s NHS clinical team.

BioMarin intends to engage the UK’s National Institute for Health and Care Excellence (NICE) and NHS England on the use of its cerliponase alfa treatment for patients with CLN2 in England. Ultimately, it is hoped that the work from BioMarin and others, supported by evidence from the Genomics England database, will bring clinicians more treatment options for patients with CLN2.

“The focus of rare undiagnosed diseases in Genomics England’s 100,000 Genomes Project provides us with a unique opportunity to better understand the clinical spectrum of devastating childhood diseases, and to develop targeted therapeutics that can impact patients and their families.  We are excited about these initial findings and about improving alignment between disease diagnosis and access to available therapeutics in the UK and around the world,” said Dr Lon Cardon, Chief Scientific Officer at BioMarin.

Legacy

These two examples highlight the range of value that Genomics England’s Discovery Forum is providing to multiple stakeholders. Access to the data is allowing drug developers to strengthen the body of clinical insights for target cohorts; in turn their work is immediately fed back into clinical reporting that Genomics England provides for Project participants through the NHS.

This work exemplifies the Discovery Forum aim to improve patient outcomes. It is a goal that relies on a variety of stakeholders working together and sharing knowledge. While the dataset is a valuable research asset, it is the researchers themselves who will define its value.

Joanne Hackett, Chief Commercial Officer, Genomics England, said: “The 100,000 Genomes Project has succeeded in its role as a pilot project for establishing a genomic medicine service through the NHS. Our ambition is to grow the legacy of the Project to improve patient outcomes across the globe. Through the Project, and in collaboration with our clinical delivery partners across the NHS, we have built an extraordinarily rich dataset that will continue to grow in breadth and depth.

“The potential applications of this are exciting. There are clear immediate benefits in developing new diagnostics technologies and data analysis tools. There are also long-term benefits that tie in with the paradigm shifts we are seeing in the pharmaceutical industry. We are leaving the age of the block-buster drug. The focus has moved to targeted therapies, drug repositioning, and reducing the failure rate of clinical trials. It is here that we see a lot of exciting potential applications of the 100,000 Genomics Project cohort data.”

Chair of the Genomics England Participant Panel, Jillian Hastings-Ward, said: “People signed up for the 100,000 Genomes Project in the hope that their data could be useful in advancing scientific discovery as well as, perhaps, helping them individually. This news demonstrates that the Project is starting to make tangible progress on both of these fronts.”

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Genomics England and industry partners complete first phase of liquid biopsy study

Genomics England has announced the successful completion of the first phase of its collaboration with Inivata and Thermo Fisher Scientific to investigate the use of liquid biopsies in cancer. This is part of a pilot project aiming to:

  • assess the suitability of circulating tumour DNA (ctDNA) samples collected by the NHS during the 100,000 Genomes Project
  • perform objective technology evaluation of the various market offerings in liquid biopsy
  • generate evidence for the potential consideration of such technology implementation in future routine healthcare for better disease treatment or prevention

Inivata and Thermo Fisher Scientific analysed around 200 blood plasma samples, donated by participants of the 100,000 Genomes Project, for their suitability for Next Generation Sequencing-based testing. The analysis also served to further establish the capacity of Inivata’s liquid biopsy platform, InVision®, and Thermo Fisher Scientific’s Oncomine™ Pan-Cancer Cell-Free Assay to identify the presence of cancer.

The results of the study showed that the plasma samples collected were of a high quality and produced reliable results when analysed. These results were consistent across all cancer types.

The collection methods were shown to allow for ctDNA analysis, opening up a range of possibilities for the further analysis of banked samples using liquid biopsy technology such as those provided by Inivata and Thermo Fisher Scientific. This demonstrates the strong potential for liquid biopsy to improve cancer management and outcomes for UK patients.

These results, and those from the two subsequent phases, will be shared with researchers in the UK and around the world providing additional multiomic data to members of the Genomics England Clinical Interpretation Partnership (GeCIP) and Discovery Forum.

The second phase of the study aims to generate data to form the basis of an objective technology assessment between pre-selected liquid biopsy companies. This will inform future procurement and research strategies to improve patient outcomes. The final phase will be a proof of concept longitudinal ctDNA sample study. This will help develop less invasive sample collection techniques, more effective monitoring processes, and ultimately better cancer care.

Clive Morris, Chief Executive Officer at Inivata, said: “We are delighted to be working with Genomics England, and to see the progress being made with this collaborative study. The successful end of this initial phase demonstrates the quality of the sample collection from all sites and will enable the exploration of a number of ways of providing further insights to patients. Inivata and Genomics England share a commitment to delivering innovations to UK patients, unlocking exciting new treatment options and improving patient care.”

Joydeep Goswami, President of Clinical Next Generation Sequencing and Oncology for Thermo Fisher Scientific, said: “The application of liquid biopsy to better understand cancer holds great promise as a less-invasive and potential early detection approach for the future of patient care. The successful completion of phase one of this program, enabled by the leadership and support from Jacqui Shaw’s lab at the University of Leicester, corroborates the potential of this approach. We look forward to the next steps in our ongoing collaboration with Genomics England.”

Mark Caulfield, Interim Chief Executive Officer at Genomics England, said: “Our priority at Genomics England is to improve patient outcomes. The potential that liquid biopsies represent for earlier diagnosis and tracking of cancer is well documented, but nonetheless remains very exciting. There is still much to do to establish clinical utility and suitability of the technology. As we continue to carry out this work, we keep in mind what this means for patients – significantly less invasive procedures, and the potential to detect cancers much earlier and treat them much more effectively.

Joanne Hackett, Chief Commercial Officer at Genomics England, said: “Exploring new and developing technologies is central to our mission at Genomics England. If we are to keep the UK a world leader in the delivery of genomic medicine, it is going to be through collaborations such as this with leading technology companies. The results of the first phase of our liquid biopsy trials are very encouraging, and we look forward to further rigorous testing through phase two.”

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