Category: Genomics England

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.”

Find out more about how we work with industry.

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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Genomics England’s PanelApp software is now open source

The software behind Genomics England’s PanelApp, a crowdsourcing platform for sharing and evaluating gene panels, has now been made publicly available for the scientific and clinical community to use. Data from the 100,000 Genomes Project will not be shared or be made open source.

By making the PanelApp software open source, scientists in organisations across the world will be able to upload their own data to create gene panels for research.

PanelApp is a knowledgebase of virtual gene panels for rare diseases and cancer. It has a crowdsourcing tool that allows experts from around the world to provide reviews of genes and the underlying evidence for what may be causing disease. These panels are publicly available to browse, download, and query.

In each panel, genes are ranked using a traffic light system.  Using specially designed software tools, the Genomics England Curation Team assess the crowdsourced expert reviews and evidence from other sources to define which genes have a high level of evidence for causation in a disease. Gene panels with strong evidence are classified as “green” for genome interpretation. The gene panels are used in Genomics England’s 100,000 Genomes Project to help prioritise genetic variants to gain diagnoses for rare disease patients, or highlight important inherited variants in cancer susceptibility genes for cancer patients. PanelApp is also being used to help support the process of gaining a consensus on which genes should be included in tests for the NHS Genomic Medicine Service.

The PanelApp software, which includes the review and curation tools described above, has been released in GitHub, making it available for the bioinformatics, research and clinical community to utilise.

What now for 100,000 Genomes Project participants?

Participant Panel Chair Jillian Hastings Ward took the opportunity to grill Genomics England’s Chief Scientist and interim Chief Executive Professor Mark Caulfield on film while both were at the Festival of Genomics in January 2019. See some of the key answers below.

What are you going to do with the data sequenced through the 100,000 Genomes Project this year?

Our first priority is to get reports back to those who have not yet received a result. Our second priority is to revisit the genomes for people who haven’t yet got an answer, to see if new knowledge or new ways in which we can analyse a genome will be able to find answers.

So far the analysis has been focusing on individual gene panels as a starting point. Can you tell us about what will happen next?

When we first started, the knowledge base meant we had to focus on genes, so we developed panels using literature known worldwide. For some people – around 40% in intellectual disability – that is making a diagnosis and getting them answers quite quickly. But we are continually evolving those panels and now we’re looking outside the genes, in other parts of the genome, for variations that might cause disease, and we are bringing them as they are invented. That’s the virtue of having your whole genome – we can go back with new knowledge to get new answers for our participants.

What is the timeframe?

We are aiming to analyse everyone’s genome for the first time and returning results back to the NHS by July 2019. Then there will be a little bit of a delay while they look at those reports and consider whether it is reliable enough to give that information back to the participants, as these clinicians are the ones caring for those patients.

Watch the video with Professor Caulfield’s full answers below:

This video accompanies a letter sent from Professor Caulfield to all participants of the 100,000 Genomes Project.

Jonathan Symonds appointed new Chair of Genomics England

John Symonds (left) and Sir John Chisholm (right)

Jonathan Symonds CBE is to be appointed the new Chair of Genomics England. Following the success of the 100,000 Genomes Project, Genomics England announces that its Chair, Sir John Chisholm will step down on 29 January 2019. Sir John, who has led the company since its inception in 2013, indicated his decision to leave to the Board once Genomics England realised its 5 year ambition to sequence 100,000 whole genomes in early December.

Jonathan Symonds has more than 30 years’ experience across a spectrum of life science enterprises. As Senior Non-Executive Director on the Genomics England Board, he has been part of Genomics England since 2014 and increasingly engaged in the oversight of Genomics England’s forward plans.

The Chief Executive of Genomics England, Professor John Mattick is to leave the company following his successful work on crafting the recently announced UK genomics vision. Genomics England’s Chief Scientist, Professor Mark Caulfield has agreed to act as interim Chief Executive. The search for a permanent appointment will begin next week.

The incoming chair of Genomics England, Jonathan Symonds said:

“Sir John Chisholm’s accomplishment has been extraordinary. His skill and visionary leadership have enabled the UK to become the leader of global efforts to harness the potential of genomic science and healthcare and to realise the potential of personalised medicine. He has worked closely with partners across the NHS, academia, and industry to create an extraordinary infrastructure for genomic research and health.

“Professor John Mattick is a formidable scientist who has argued passionately that genomic medicine can transform medical research and healthcare and has helped us build an ambitious vision for the role genomics can play in the future of healthcare. We would like to thank John for the contribution he has made to Genomics England and we wish him well for the future.

“As we look to the next phase of Genomics England, in partnership with the NHS, to deliver genomics based diagnostics in clinical care, I’m delighted to announce that Professor Mark Caulfield, who as chief scientist directed much of the work of the 100,000 Genomes Project, will act as our interim CEO. Mark will head Genomics England as we rise to the challenge of speeding up diagnosis and personalised treatments through the NHS with the Genomic Medicine Service and keep the UK at the leading edge of genomic medicine and science.”

Jonathan Symonds added:

“I am delighted to accept the honour of becoming Genomics England’s Chair. Sir John’s shoes will be hard to fill.  We have an exciting challenge ahead in partnership with the NHS, as we continue our efforts to prevent disease, unlock new treatments, improve and accelerate diagnosis and to help patients receive the best care tailored to their needs.”

Sir John Chisholm said:

“I am so proud and pleased with the extraordinary achievement of realising our ambition of sequencing 100,000 whole genomes within the NHS. And this felt like the right time for me to move on. It was an unprecedented team effort involving thousands of researchers, clinicians and others across the NHS, academia, industry, and beyond. Most especially thanks to the generosity of more than 93,000 NHS patients and their family members who continue to put their faith in Genomics England as the work to push back the boundaries of genomic science and healthcare goes on.”

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

 “We should all be incredibly excited about the potential for genomics to improve the lives of patients and transform healthcare – and I’m proud that the UK is leading the world in this area. Sir John Chisholm has been paramount in the success of the 100,000 Genomes Project and I want to thank him for his inspiration and hard work. I welcome Jonathan Symonds CBE to drive forward the next stage of British global leadership in genomics and look forward to working with him to deliver our commitment to sequence one million whole genomes over the next five years – helping improve peoples’ lives.”

Lord David Prior, the Chair of NHS England said:

“The delivery of the 100,000 genomes project within a working health system is an achievement which is viewed in awe all over the world. It was only possible due to the close partnership between Genomics England and NHS England. We have in Jonathan Symonds an enormously accomplished Chair to take over from Sir John Chisholm. I look forward to working with him and Professor Caulfield to tackle the delivery of even more benefit for patients, science and industry from the next 5 year vision. This is almost certainly the biggest breakthrough in clinical practice in my life time, it makes predictive and personalised medicine a reality.”

Professor John Mattick said:

“I am very sorry to be leaving Genomics England at this time. Genomics England has an exciting future through its partnership with NHS England to deliver personalised medicine, and fuel innovation and investment in genomic medicine. I am pleased with the contribution I was able to make in developing the vision for the next 5 years that the Secretary of State announced in October, and in laying out a plan to achieve this vision. I wish Professor Mark Caulfield and all the staff at Genomics England well with their future endeavours.”

The journey to 100,000 genomes

Genomic potential

Pinpointing the beginning of the 100,000 Genomes Project isn’t easy. It could be argued that Crick, Franklin and Watson started it all in 1953; or Frederick Sanger’s pioneering sequencing technologies in the late ‘70s; perhaps the Human Genome Project in 2003; or even the UK10K project in 2008. Our journey, however, began in 2012 with the announcement of the Project and, in 2013, the creation of Genomics England to drive it to completion.

The background to the odyssey was a recognition that advances in genomics, informatics and analytics brought closer the possibility of more precise diagnosis, alongside personlised and targeted treatments. In 2012 science could see the potential to identify the underlying cause of disease, predict how a person might respond to specific interventions and determine who was at risk of developing an illness.

The stumbling block? Nobody had ever tried.

Building a genomic medicine infrastructure

The UK was brave enough to lead the way – announcing the groundbreaking 100,000 Genomes Project, which aimed to sequence 100,000 whole genomes from around 70,000 participants with rare disease, their families and people with some cancers. The decision was backed by robust government support – both political and financial – which included over £300 million of investment.

Building a genomic infrastructure – partnership on an industrial scale

As we celebrate the sequencing of the 100,000th whole genome just five years later, it is important to remember the scale of the achievement. For those of us here at the beginning, the prospect was simultaneously exciting and daunting. We were asked to not only sequence an unprecedented number of whole human genomes, but also to plug this in to the rich health data held by the NHS. With important objectives to create a consent-based and transparent programme that fostered an emerging UK genomics industry – our ultimate aim was to bring real and lasting change to NHS care.

The challenge, described by one colleague as “building the plane whilst flying it”, was to create the infrastructure for genomic medicine from scratch, whilst also delivering on our objectives. A more traditional model would have seen us build the machinery first and then begin sequencing: the 100,000 Genomes Project did both simultaneously. It was a Project that demanded partnership on an industrial scale – and would never have been delivered without the support of thousands of organisations and individuals.

Genomics England began its close relationship with NHS England to recruit the first participants in 2014. In the same year, NHS England created 11 Genomic Medicine Centres (GMCs), eventually growing to 13 in 2015, and today joined by organisations in Northern Ireland, Scotland and Wales.

GMCs work across areas of 3 to 5 million people in over 85 NHS trusts. They have been key components of the project: recruiting and consenting patients; providing DNA samples; developing the mechanisms for validating results; and working to feed back results to participants. We cannot underestimate the commitment, skill and hard work of thousands of NHS staff who have pioneered these GMCs and the cause of genomic medicine in the NHS.

At the start of 2015, another piece of the infrastructure puzzle fell into place with the opening of the NIHR Biosample Centre to store samples from the Project. And just two months later, we established the Genomics England Clinical Interpretation Partnership (GeCIP). GeCiP brings together thousands of researchers and clinicians from across the world – granting them carefully controlled access to our database to power new discoveries in genomic medicine. Today GeCIP research covers 42 areas – known as ‘domains’ – including rare cardiovascular and neurological disorders, and cancers such as breast, lung and ovarian.

Early in the Project, we realised that many of the technologies and services needed to deliver genomic medicine simply didn’t exist – and if we wanted them we would have to build them. One of these technologies was the bioinformatics pipeline, which is critical to ensure processing at the scale in the world’s largest publicly funded health system. It has involved a huge commitment from our bioinformatics team and others – but has resulted in one of the world’s few semi-automatic bioinformatics pipelines.

This ‘if you can’t buy it, build it’ approach has seen a range of innovations. Work with our sequencing partner, Illumina, for example has acted as a significant catalyst in reducing the costs of sequencing: from billions in 2003 to around £600 today and around £100 in the not too distant future. We have also created a bespoke, multi-petabyte storage environment to cope with the grand challenge of managing a large scale whole genome and clinical dataset.

In 2015 we also began to explore how to align our work with the needs of industry – the companies that will eventually turn genomic discovery into routine treatments. This started with the GENE Consortium, which evolved in 2017 into the Genomics England Discovery Forum we see today. The Forum is a platform that allows us to bring together charities, patients, researchers, clinicians and others with industry partners to share perspectives and better understand how to speed discoveries from the laboratory bench to the patient’s bedside. In the past few months, the value of the Forum has been demonstrated with members discovering previously undiagnosed patients in our database – with the hope that this will lead to better diagnosis and the development of more effective treatments.

People powered healthcare

From the outset, the Project recognised that genomic medicine could not succeed without the understanding, trust, acceptance and consent of patients. Genomic medicine is truly “people-powered healthcare”. It heralds a changing relationship between the patient and the NHS, with a new consent model where healthcare and research become indivisible. It is important to understand that new technology and the use of data will only be socially and clinically enabled if it is trusted by the patient.

100,000 Genomes Project timeline

In 2016 Genomics England established the Participant Panel, which acts as an advisory body to our Board. The Panel is at the heart of our decision making processes, with members sitting on the Access Review Committee, the Ethics Advisory Committee and the GeCIP Board. Involving participants at this fundamental level ensures that the Project is always responsible to the people who drive it.

It also underlines the importance of the Project to participants. Participant Panel Deputy Chair, Rebecca Middleton, has said, “The Project brings me something new – hope. Whether in 5 or 15 years, new genomic discoveries may be able to help me.”

Ensuring that we are able to gain the trust of patients demands that we understand their attitudes to genomic medicine – and this inspired the ‘Genomics Conversation’ in 2016. The Conversation is a genuine engagement project – not seeking to influence its audiences, but rather to listen.

And what is it that patients get from the investment of their trust, understanding and consent?

Even at this early stage, genomic medicine is helping to transform cancer services – making real progress in providing DNA of sufficient quality for whole genome sequencing – an issue that has hampered efforts to apply genomics in cancer diagnosis and treatment around the world. NHS England is re-aligning its laboratory services as it moves from formalin-fixed paraffin embedded (FFPE) to Fresh Frozen (FF) sample handling.

The first participants received their diagnoses in February 2015, when we had sequenced around 2,000 whole genomes, with the first diagnosis of children made in January 2016.

As we have moved to 100,000 genomes, the number of people has grown. People like Project participant Alexander and his family who in finally receiving a diagnosis for LEOPARD Syndrome can now finally know what is wrong and seek support from others living with the same disease. Fellow participant, Jessica, and her family discovered that her condition is caused by errors in the SLC2A1 gene that cause ‘Glut1 deficiency syndrome’ – which only affects around 500 people worldwide. Jessica’s diagnosis has opened up the potential for highly tailored treatments.

Beyond 100,000 genomes

The 100,000 Genomes Project has been a real innovation – from bioinformatics to computing to storage to research to industry partnership to public engagement. As our learning and dataset grows, so too will our ability to better diagnose and treat an ever expanding number of diseases. Whilst the UK is now an acknowledged leader in population genomics, this is a truly global effort – with the potential to bring patient and economic benefit across the world.

The Secretary of State of Health and Social Care’s announcement on 2 October laid out an exciting roadmap for genomic medicine. His words demonstrate the importance of personalised medicine and its ability to continue to deliver cutting edge care within the NHS: “I’m proud to announce we are expanding our 100,000 Genomes Project so that one million whole genomes will now be sequenced by the NHS and the UK Biobank. I’m incredibly excited about the potential for this type of technology to improve the diagnosis and treatment for patients to help people live longer, healthier lives – a vital part of our long-term plan for the NHS.”

The lasting legacy of the 100,000 Genomes Project is the NHS Genomics Medicine Service that began to roll out at the beginning of October 2018. The Project has proven the concept of genomic medicine at scale and built the infrastructure that underpins the GMS. Genomics and the GMS are transformative, poised to change the way future of healthcare is delivered. As we reach the 100,000 genome milestone, we are at a tipping point in medicine that will usher in an era of highly personalised medicine – which may consign generic drugs and treatments to medical history.

Getting to this point has been a demonstration of the power of partnership. We are only here because of the thousands of patients and their families who have placed their trust in a project at the cutting edge of healthcare. Working with them have been many thousands of NHS staff who worked tirelessly to not only deliver the Project, but in many cases, pioneer totally new systems, processes and procedures to ensure that genomic medicine can become part of routine NHS care. And beyond them there is the vast and rich ecosystem of charities, industry partners, funders, government organisations and a host of others. To everyone – we would like to say “thank you”.

Whatever its history and whenever it began, we can be sure that the genomic medicine journey is just beginning – and its future will be an exciting one.

The UK has sequenced 100,000 whole genomes in the NHS

Pioneering 100,000 Genomes Project reaches its goal and thanks all involved

Health Secretary Matt Hancock has today announced that the 100,000 Genomes Project, led by Genomics England in partnership with NHS England, has reached its goal of sequencing 100,000 whole genomes from NHS patients.

This ground-breaking programme was launched by then-Prime Minister David Cameron in 2012, with the goal of harnessing whole genome sequencing technology to uncover new diagnoses and improved treatments for patients with rare inherited diseases and cancer. The task was to make the UK a world leader within five years.

The 100,000 Genomes Project has delivered life-changing results for patients with one in four participants with rare diseases receiving a diagnosis for the first time, and providing potential actionable findings in up to half of cancer patients where there is an opportunity to take part in a clinical trial or to receive a targeted therapy.

To do this Genomics England worked with NHS England to create 13 NHS Genomic Medicine Centres (GMCs) to support the project, a state-of-the-art sequencing centre run by Illumina, Inc. and an automated analytics platform to return whole genome analyses to the NHS.

Genomics England and NHS England are extremely grateful to the 85,000 participants, 1,500 NHS staff, over 3,000 researchers, the National Institute for Health Research and the UK Government whose support and funding have been key to the success of this pioneering NHS transformation programme.

As a result the UK has become the first nation in the world to apply whole genome sequencing at scale in direct healthcare, as well as providing access to high quality de-identified clinical and genomic data for research aimed at improving patient outcomes.

The project has laid the foundations for a NHS Genomic Medicine Service, which will provide equitable access to genomic testing to patients across the NHS from 2019.

Health Secretary Matt Hancock said:

Sequencing the 100,000th genome is a major milestone in the route to the healthcare of the future. From Crick and Watson onwards, Britain has led the world in this amazing technology. We do so again today as we map a course to sequencing a million genomes. Understanding the human code on such a scale is part of our mission to provide truly personalised care to help patients live longer, healthier and happier lives.

I’m incredibly excited about the potential of this type of technology to unlock the next generation of treatments, diagnose diseases earlier, save lives and enable patients to take greater control of their own health.

Sir John Chisholm, Chair of Genomics England, said:

At launch the 100,000 Genomes Project was a bold ambition to corral the UK’s renowned skills in genomic science and combine them with the strengths of a truly national health service in order to propel the UK into a global leadership position in population genomics. With this announcement, that ambition has been achieved. The results of this will be felt for many generations to come as the benefits of genomic medicine in the UK unfold.

Professor Mark Caulfield, Chief Scientist at Genomics England, said:

The sequencing of 100,000 whole genomes marks an extraordinary UK achievement that is transforming the application of genomics in our NHS. Genomics England will continue to analyse these genomes alongside life course clinical information to reveal answers for as many participants as possible and improve their NHS care. With the generous support of our participants, the NHS, the National Institute for Health Research and the Government we will continue to ensure the UK’s global leadership in genomic healthcare.

 Professor Dame Sue Hill, Chief Scientific Officer for England and Senior Responsible Officer for Genomics at NHS England, said:

This achievement has only been possible because of the amazing commitment and contribution of NHS teams across the country and I would like to thank each and every one of them for rising to this challenge and excelling in its delivery.

The results, which will continue to be returned to patients, show how genomic medicine can transform lives, bringing quicker and better diagnoses and increasing the number of patients surviving cancer, and the opportunity now is for the NHS to turn this research into reality by introducing sequencing technology as part of our world-leading NHS Genomic Medicine Service.

 Jillian Hastings Ward, Chair of the National 100,000 Genomes Project Participant Panel, said:

This is a fantastic milestone. Thanks to the dedication and hard work of the whole project team, patients and their families are starting to receive life-changing diagnoses. We look forward to seeing more results in the near future – for the rest of the project participants, and for the wider public who will soon benefit from genomic medicine in the NHS. We will also keep working with Genomics England to make sure they keep patients’ interests at the heart of all they do.

Francis deSouza, President and CEO of Illumina, Inc., said:

We congratulate Genomics England and the NHS for reaching this historic achievement and are honored to be part of it.  The accomplishment of the 100,000th genome is only the beginning in many respects, but a significant step towards realizing the promise of genomic medicine to develop products for earlier detection and treatment of many rare diseases and cancers.

James Fenton, Project Manager at the NIHR National Biosample Centre – the facility that stores and processes samples for the 100,000 Genomes Project – said:

It has been a unique study to have been part of and a fantastic achievement on all fronts, really demonstrating that the UK is leading the way in genomic research towards personalised medicine. This milestone is testament to the hard work and dedication put in by all at National Institute for Health Research National Biosample Centre and our partners in Genomics England, the NHS GMCs and Illumina.

A platform for progress – driving genomic vision, research, innovation and outcomes – a blog from Joanne Hackett

Joanne Hackett, Genomics England Chief Commercial Officer, explores how November’s 4th Discovery Forum is helping to shape a genomics vision, research, innovation and outcomes.

Forum members come together at the MUFG sponsored breakfast session.

Back in the summer I spoke of my pride in the Discovery Forum’s progress just a year after its inception. In this blog, I want to demonstrate what this really means in practice.

The Forum came together on 8 November with a truly heavyweight agenda. As I’ve said before, this isn’t a talking shop, but a powerful platform to deliver on the promise of genomic medicine – both for patients and the economy.

It was an agenda that looked at a developing genomics vision, real-world research opportunity, the potential to foster innovative industry and emerging outcomes.

Vision

As we rapidly approach the sequencing of the 100,000th genome and the completion of Genomics England’s genuinely historic ‘first phase’ – NHS England’s Chief Scientific Officer, Professor Dame Sue Hill, and our Chief Scientist, Professor Mark Caulfield, discussed the next ‘new horizon’.

This was heralded by the Secretary of State for Health and Social Care, Matt Hancock, on 2 October. He outlined the roadmap that will take us from 100,000 genomes to a million – and beyond. It’s an exciting vision built on a tremendous achievement: in a little more than 5 years, Genomics England has scaled genomics into a global sector and supported NHS England in delivering its world-leading Genomics Medicine Service (GMS).

Research

Sessions on collaboration saw representatives come together from across the genomics space – including data companies, our own GeCIP research initiative and the charity sector – to see how we can improve the ways we mine data to yield discovery.

David Dexter, Deputy Director of Research at Parkinson’s UK, presented to the Forum on the power of collaborations between academia, industry, patient groups and charities to realise the potential of genomic medicine – and support smarter and more effective clinical trials. A key theme was the need to integrate different datasets – including imaging, clinical and genomics data – to help drive stratification and personalised approaches.

Taking this collaborative theme forward, discussions also covered progress in the Genomics England Clinical Interpretation Partnership (GeCIP) – and the emerging cross-cutting opportunities this offers.

Tying the collaborative theme together, we heard from companies that are focused on how to integrate data sources and derive maximum impact. Artificial intelligence (AI) specialist NVIDIA presented on the opportunities of deep learning and data engineering. IQVIA explored the development of a platform to better-connect clinical and de-identified genomics data. The objective of the platform is to deliver robust evidence that fuels faster and more efficient drug research – which will, in turn, accelerate discoveries and their translation into routine genomic treatments.

Innovation industry

The next link in the genomics chain is the development of innovative start-ups to fully harness the medical value of data.

The Francis Crick Institute’s Veronique Birault spoke to the Forum about its KQ Labs programme – aimed at accelerating high growth start-ups in the data-focused biomedical sector. KQ Labs offers fast-emerging companies real-world support, with financial grants backed by an ecosystem of global experts, covering areas that include entrepreneurship, the health sector, data science and investment.

Carrying this forward, discussion then moved on to how the Forum can support this and other initiatives – as well as start-ups themselves. Members heard from innovative, genomics-focused companies including Lifebit, Pangaea, Sevenbridges, Alexion, Mendelian, Sensyne Health and Repositive.IO.

And of course, funders were here too – with the presence of innovation specialist MUFG, which gave financial focus and insight to discussions.

Outcomes

All of this activity is hugely positive, but leaves out the final link – outcomes. So it was hugely encouraging to see rare disease-focused biopharma Forum members Alexion and BioMarin present on progress they had made using selected and de-identified data from the Genomics England dataset.

Alexion and BioMarin have identified previously undiagnosed patients with life threatening kidney (CLN2) and neurological (nephronophthisis) conditions respectively. Their work is important because, in identifying the exact cause of these conditions, there are opportunities to develop ever more effective and targeted treatments – which may delay their progression or even prevent the disease.

The November Discovery Forum was genuinely meaningful – and is helping to shape activity as we move along the genomic roadmap. Its collaborative and inclusive approach means we are able to explore genomics holistically – making it a real platform for progress. I can’t wait to see where the next Discovery Forum will take us.

Helomics partners with Genomics England’s Discovery Forum to drive precision medicine for ovarian cancer

Helomics, a personalised healthcare company whose mission is to improve the standard of care for cancer through innovative precision oncology products and boutique CRO services, and Genomics England announced today that Helomics has become a full Discovery Forum partner. Helomics will utilize the rich de-identified genomics and clinical data set for the 100,000 Genomes Project to further develop its artificial intelligence-based precision oncology platform for ovarian cancer.

The 100,000 Genomes Project is a groundbreaking initiative, sequencing whole genomes of National Health Service patients with rare diseases and their families, as well as patients with common cancers. The aim is to transform healthcare through new diagnoses and personalized treatments. The Precision Medicine Market is set to exceed USD 96 billion by 2024; according to a research report by Global Market Insights, Inc. Helomics continues to be an innovative precision medicine company that will continue to show growth in this robust market in 2019 and beyond.

“We are excited to partner with Genomics England and gain access to the rich, de-identified, genomic and clinical data of the 100,000 Genomes Project. We intend to apply our state-of-the-art machine learning to this dataset to expand the capabilities of our precision oncology platform, which helps oncologists offer individualized treatment options for ovarian cancer patients. We anticipate this to be the first of several projects, leading ultimately to bringing the benefits of Helomics precision oncology to ovarian cancer patients within the NHS,” commented Gerald Vardzel, President and CEO of Helomics Corp.

Expanding on the scientific goals of the project, Dr. Mark Collins, VP of Innovation and Strategy at Helomics, said:

The promise of precision oncology is therapy tailored to the patient’s own cancer, yet the reality is that while we can identify alterations in the DNA of the patient’s tumor most of these mutations are not actionable with current drugs. The goal of this project is to combine genomic profiling of the patient tumor (from the Genomics England data), with the drug response of the patient’s own tumor, grown in the laboratory (Helomics unique dataset), utilizing the power of machine learning to create a “virtual” model of the tumor. We can then use this model to guide the oncologist in selecting appropriate standard of care drugs to best treat the patient, as well in partnership with pharma companies to develop the next generation of precision therapies.

Commenting on the new Discovery Forum Partner,  Joanne Hackett, Chief Commercial Officer of Genomics England, said:

We’re delighted to work with Helomics and their precision oncology products to maximize the benefits to patients. As part of the Discovery Forum, Helomics will collaborate with other companies at the forefront of genomics and technology, to ensure that we turn research findings into treatments, diagnostics and benefits for patients as soon as possible.

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