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:
Nicola Blackwood, Health Minister said:
Professor Sir Mark Caulfield, Chief Scientific Officer of Genomics England said:
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.
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:
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’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.
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.
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.
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:
Jacqui Gath, cancer survivor and patient advocate (ICPV/YHCRP), said:
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:
John Norton, Citizen Partner of Discover-NOW said:
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.
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.
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:
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:
To tell the story behind the numbers, we put a few questions to Dr James Holman, Research Environment Project Lead.
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.
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:
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:
Matt Hancock, Secretary of State for Health and Social Care, said:
Baroness Blackwood, Parliamentary Under Secretary of State, said:
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.