The 100,000 Genomes Project team at London North West Healthcare NHS Trust celebrated International Rare Disease Day by hosting a stall at Northwick Park Hospital, to raise awareness of the Project among patients and staff. Scientists from the genetics laboratory were also on hand, to explain the recent advances in genomic technology and whole genome sequencing.
It was a fantastic day, and demonstrated the improved healthcare opportunities now available to people with rare diseases. Likewise, there were good news stories of people who have received a diagnosis through participating in the Project. Doctors from different specialties were also shown how to refer patients for recruitment, helping to integrate genomic medicine into routine patient care. The news that such a service-transforming project was underway within the Trust was received with a great deal of enthusiasm.
People in Scotland with rare genetic diseases are set to benefit from a DNA study that seeks to improve their diagnoses and treatments.
The study – launched by the Scottish Genomes Partnership in collaboration with Genomics England – will analyse the entire genetic make-up of 330 people with rare diseases and members of their family.
Using advanced computing to link genetic data with patients’ health information, scientists hope to pinpoint differences in their DNA code that may be responsible for their condition.
The research aims to offer more precise diagnoses for patients and explore how whole genome sequencing technology could be used in clinical practice to improve treatment and management of the diseases.
Participants will be identified by NHS Scotland Genetics Clinics and invited to take part in the research along with members of their close family.
A total of 1,000 people will have their genome sequenced for the research, which will contribute to the 100,000 Genomes Project, a flagship project to advance clinical care through genome research.
Around 3.5 million people in the UK are living with a rare disease caused by a faulty gene, such as muscular dystrophies, rare forms of intellectual disability and rare inherited neurological problems. Although each disease affects fewer than one in 2,000 people in the population, there are between 6,000 and 8,000 known conditions which are often chronic and life-threatening. Doctors are describing new disorders every day but many people still do not receive an accurate diagnosis for their condition.
The study will take advantage of cutting-edge whole genome sequencing technology at the Universities of Edinburgh and Glasgow, advanced computing facilities at the University of Edinburgh and analytical expertise at Genomics England.
Health Secretary Shona Robison said: “I am pleased that the Scottish Government is supporting this initiative together with the Medical Research Council. The launch of this study is a significant milestone towards embedding use of this cutting-edge technology by NHS Scotland to benefit patients with rare genetic diseases.”
Professor Tim Aitman, Co-Chair of the Scottish Genomes Partnership and Director of the University of Edinburgh’s Centre for Genomic and Experimental Medicine, said: “Genomics has come a very long way since the publication of the first human genome in 2001. This collaboration enables the investment made by the Universities of Edinburgh and Glasgow in the latest genome sequencing technology to make a direct and immediate impact on the healthcare of patients in Scotland. We look forward to working on this ground-breaking project with our partners in NHS Scotland and Genomics England.”
Professor Zosia Miedzybrodzka, Professor of Medical Genetics at the University of Aberdeen and NHS Grampian, and Chief Investigator of the study said: “The clinicians and scientists delivering NHS Scotland Genetics Services are delighted that patients in Scotland with undiagnosed genetic conditions will have this opportunity to benefit from finding out the cause of their health problem.”
Dr Marion Bain, Medical Director of NHS National Services Scotland said: “Cutting edge techniques and equipment mean that it is now possible to sequence an individual’s genome in a matter of days. As the cost of sequencing comes down, new analytical techniques are developed and our knowledge in this area grows, there is huge potential to develop more effective and cost-effective diagnostic and treatment services.”
Professor Mark Caulfield, Chief Scientist at Genomics England said: “I am delighted that patients living in Scotland will have the opportunity to benefit from genomic medicine by taking part in the 100,000 Genomes Project. Our aim is to bring new diagnoses for patients with rare disease and enable better treatments for patients across the UK.”
Alastair Kent, Genetic Alliance UK said: “Whole genome sequencing has become an invaluable route for patients and families to be able to receive an accurate and timely diagnosis of their condition. The 100,000 Genomes Project has helped many families in England to understand their situation and plan for what awaits them. The development of the Scottish Genomes Partnership, and the linkage with Genomics England is very good news for Scottish families and for the whole rare disease community across the UK. We look forward to a long and productive collaboration that will boost research and bring exciting possibilities for patient benefit closer to being realised.”
The Scottish Genomes Partnership is a collaboration between the Universities of Edinburgh, Aberdeen and Glasgow, four regional Clinical Genetics Units and four Genetic laboratories commissioned by NHS National Services Scotland. It is funded by the Scottish Government and the Medical Research Council.
Rare disease is a deceptive term. There are 6,000 to 8,000 different rare diseases. So although each one is rare, as a group they are common. So much so, that 1 person in 17, or 7% of people are affected by a rare disease.
About 80% of rare diseases have a genetic cause. The cause is often a single changed ‘letter’ amongst the 3.2 billion letters of DNA
that make up the human genome. Finding that one crucial change is often like finding a needle in a haystack. This first step – identifying the cause of the disease – has remained challenging until now for most rare diseases. In turn, this has prevented medicine from answering the obvious next questions for rare disease patients: what should I expect in the future? Why has the disease happened? Is there a way of curing my disease or any hope of doing so in the future? Will my child have the disease?
The 100,000 Genomes Project is an opportunity to break the mould for patients in the NHS. We are sequencing DNA from patients with rare conditions and their relatives. We aim to find the cause of the condition for people who medicine has failed to diagnose until now.
No-one has ever attempted whole genome sequencing on this scale before. Much of our work until now has been in establishing the tools and infrastructure we need to deliver results to hundreds of participants a week.
Professor Mark Caulfield, Chief Scientist at Genomics England, said:
“Thank you – to all of you affected by rare disease who have joined the 100,000 Genomes Project. Without your involvement we wouldn’t have been able to make this ground breaking project happen. We have spent many months building our new semi-automated results pipeline. This world first means that in future rare disease patients’ genome sequences can be analysed automatically. This is a key step in making sequencing available for anyone with rare disease who needs it. But it’s been complex and has taken much longer to build than we thought and we know many of you are still waiting to receive your results and feedback. Thank you for bearing with us. The good news is over 1,300 results have been released to NHS Genomic Medicine Centres. They now have to be double checked by the NHS (validated) but we are finally getting there. Thank you from all of us.”
By Sir John Chisholm, Executive Chairman, Genomics England.
As many NHS Genomic Medicine Centres are gearing up to organise local activities to mark Rare Disease Day next week (28th February), the 100,000 Genomes Project is making great progress. All thirteen NHS Genomic Medicine Centres are recruiting rare disease and cancer patients to the Project, and initiatives in Scotland, Northern Ireland and Wales have agreed to join us in this world leading programme.
Scientist working at an Illumina sequencing machine, Ogilvie building, Wellcome Genome Campus, Cambridge.
Counting the genomes from the (NIHR) BioResource – BRIDGE Studies (which started before Genomics England but whose genomes were always planned to be part of our dataset) we are delighted to have sequenced over 26,000 whole genomes, with over 19,000 in our datacentre.
Together with genomes from Scotland, Northern Ireland and Wales, we know we will certainly exceed the 100,000 target. But actually the bigger picture is no longer simply sequencing 100,000 human genomes linked to quality clinical data. The big picture is building the infrastructure for routine commissioned genomic medicine in the NHS. It is building a unique research database, thus enabling a powerful learning system able to provide better outcomes for patients. It is that vision which motivated the then Chancellor of the Exchequer in the 2015 Autumn Statement to allocate funds to our project stretching into 2020.
To fulfil this vision we are always working at the edge of known science. We have made good progress, but as with all scientific research, it takes time to get it right. This is why Genomics England, the Department of Health and NHS England have all agreed that the project will be extended from 2017 until the end of 2018. We spent a large part of the past year developing a world class semi-automated pipeline that will enable us to feedback reports to the NHS at scale. The work on cancer genomics has been cutting-edge and the UK is leading the world in ensuring that we collect quality samples suitable for sequencing in an everyday hospital setting. This is part of the transformational aspect of the programme, ensuring that the NHS can accommodate genomic medicine in routine healthcare in the future. Together with the initiation of routine commissioning we expect to pass the 100,000 mark some time in 2018.
Professor Sir Mike Stratton & Prime Minister Theresa May. Credit – Sanger Institute, Genome Research Limited.
We will continue to deliver at pace and deliver sequences as early as possible whilst ensuring we maximise the scientific learnings from the project which will help healthcare of the future. Providing a really important dataset to our industry partners is crucial. When the Prime Minister came to the opening of our Sequencing Centre in Hinxton she led a round table discussion focused on how the country could get maximum benefit from the world lead we had established in population sequencing.
There is plenty of work ahead, and we will continue to work on developing the infrastructure required to ensure frontline clinicians can make the most of the knowledge that genomics provides, for patients now and in the future. This includes creating the interpretation and reporting ecosystem for the NHS.
The 100,000 Genomes Project puts the UK at the forefront of using genomic technology to transform patient care. We owe enormous thanks to the hard work of all those involved; to the Government, for its support in this ambitious project, and especially to our participants for their generous consent and involvement.
Genomics England today announce that it has selected QIAGEN’s HGMD® Human Gene Mutation Database for the 100,000 Genomes Project. HGMD is the leading content knowledgebase for interpretation of genomic data in hereditary and rare diseases, providing a deep resource of expertly curated data from the world’s scientific and clinical literature.
The 100,000 Genomes Project will use QIAGEN’s HGMD Online Professional solution, which is part of the QIAGEN Clinical Insight (QCI) portfolio of solutions for the interpretation of complex genomic data, to support scientists, clinicians and researchers in 13 NHS Genomic Medicine Centres for clinical reporting and interpretation.
“Rare and hereditary diseases can lock patients, families and healthcare providers in a long, difficult diagnostic odyssey, and 100,000 Genomes is a cutting-edge NHS program to gather and analyze whole genomes from a large cohort of patients in search of causes and future treatments,” said Dr. Laura Furmanski, Senior Vice President and Head of QIAGEN’s Bioinformatics Business Area. “We are honored to deepen our collaboration with Genomics England. QIAGEN’s industry-leading bioinformatics solutions, including cloud-based HGMD content, will help 100,000 Genomes derive actionable insights from a massive pool of next-generation sequencing data. We are pleased to be selected.”
“We are delighted to work with QIAGEN’s bioinformatics solutions as a comprehensive resource for manually-curated analysis and interpretation content. High-quality interpretation of genomic data in the 100,000 Genomes Project will provide deeper insights into rare inherited diseases, and ultimately lead to more diagnoses and tailored treatments for patients”, said Dr. Augusto Rendon, Director of Bioinformatics for Genomics England.
QIAGEN Bioinformatics offers a portfolio of industry-leading solutions for the analysis, interpretation and reporting of biological data. Products include Ingenuity, CLC bio and OmicSoft software and databases. As part of the QIAGEN Knowledge Base, HGMD is the gold standard for expertly curated content from peer-reviewed publications on human inherited disease mutations. HGMD has been cited in more than 5,000 scientific publications. For more information, please visit http://www.qiagenbioinformatics.com.
Today (12 January 2017), Intellia Therapeutics has joined the Genomics England Genomics Expert Network for Enterprises (GENE) Consortium, as the first dedicated genome editing company to participate in the 100,000 Genomes Project.
The GENE Consortium, established in March 2015, is the 100,000 Genomes Project’s industry partnership. Intellia will join 12 other companies who are working together in a pre-competitive trial. The collaboration aims to identify the most effective and secure way of bringing industry expertise into the 100,000 Genomes Project to realise future potential benefits for patients affected by rare diseases or cancers. Members of the consortium are granted controlled access to aggregated, de-identified genome and health data of participants. They work alongside experts that specialise in data analysis, so that the project can benefit from cutting edge advances in handling Big Data.
Genomics can greatly improve our understanding of health and disease, unlocking new treatments or repurposing existing treatments based an individual’s genomic makeup; so-called personlised medicine.
Sir John Chisholm, Executive Chairman, Genomics England, said: “The potential for genomics to transform healthcare, from better diagnoses to new drugs and treatments, is extraordinary. We are delighted to welcome Intellia Therapeutics to our GENE Consortium. The UK is a global leader in population sequencing and it’s important for the future of medicine that we continue to attract and collaborate with the most innovative emerging technologies in this space.”
“Access to genomics information is critical as Intellia looks to better understand the basis of disease and to develop potential genome-editing treatments,” said Intellia’s Chief Executive Officer and Founder, Nessan Bermingham, Ph.D., “We look forward to actively participating in the GENE Consortium, as Genomics England is enabling scientific exploration and key medical insights that ultimately will benefit patients.”
By Vivienne Parry OBE, Head of Engagement at Genomics England
When we began the 100,000 Genomes Project, our initial engagement work was with potential participants, affected both by rare disease and cancer. We wanted to know what their principal concerns were. They turned out to be both practical – for instance, what the impact of results might be on their families or if they might be disadvantaged financially by taking part – and ethical, such as use and access to their data. We made sure that we addressed these issues in our subsequent patient literature and other support material. We continue to work with participants through our Participant Panel. They are involved in many different aspects of the Project’s work. For instance, project participants sit on the group that considers applications to access the 100,000 Genomes dataset.
Identifying the key issues
For most patients, the use of genomics in medicine has clear benefits; for diagnosis, greater understanding of their condition and for the development of new treatments, not for them but for others like them in the future. Their views about the issues raised by genomics are coloured by their own experience and are different to those of the general public. But for genomics to be transformational, we need the wider public to be comfortable that the issues raised have been debated and where necessary, addressed. We also needed to know where to focus our engagement efforts in the future.
But before we began, we wanted to find out how people talked about the issues raised by genomics and what words and language would help them. Social scientist and genetic counsellor Dr Anna Middleton carried out a series of focus groups discovering that people knew more than they thought they did, even if they couldn’t explain it in correct technical terms. Her findings were translated into a series of six films, developed by advertising guru Julian Borra. Online audiences were then able to comment in order to find out what terms and language resonated best with wider audiences. You can find the films here and tell us what you think.
The results of the Genomics Conversation are fascinating and there is a full report here which I urge you to read. There is plenty of nuance as you would expect but there are also some universal red lines. One example is that insurers and marketing companies should not be allowed to access an individual’s genomic data.
We have outlined our next steps:
We need to bridge the gap between how professionals speak about genomics and how the public talk about it
We need to begin a major programme of work with cancer patients and with older people (the group most likely to be diagnosed with cancer) to find out if their views are different to those of rare disease patients and how best to tailor communications material for them
Commercial access to the 100,000 Genomes Project data is critically important if new medicines and treatments for patients are to be developed. We need to work with industry and with other partners to build trust, showing how industry develops medicines and diagnostics.
We are entering a new era of medicine. We must make sure that we both understand and address the concerns of the public and that we earn and continue to retain their trust in this transformational medical advance.
By Dr Caroline Benjamin, National Service Evaluation Project Lead and Guild Senior Research Fellow, University of Central Lancashire
Earlier this year, I and colleagues from NHS Genomic Medicine Centres were asked to deliver an evaluation with the aim to further improve the quality of the consent process and materials in the 100,000 Genomes Project.
On behalf of the project team leads, Markella Boudioni (Imperial College London), Eliot Marsden and Antje Lindenmeyer (University of Birmingham), I am pleased to present the results from ‘The National Service Evaluation of the Consent Process and Participant Materials used in the 100,000 Genomes Project’. This evaluation has been a collaborative effort, led by the North West Coast Genomic Medicine Centre, between the Genomic Medicine Centres, Universities, NHS England and Genomics England. We would like to thank the 100,000 Genomes Project participants, recruiters and focus group members who provided feedback.
Today (21st November) Genomics England, Illumina, and the Wellcome Trust Sanger Institute hosted the UK Prime Minister, Theresa May, at the opening of the Bridget Ogilvie Building on the Wellcome Genome Campus in Cambridge. This is where DNA sequencing for the 100,000 Genomes Project takes place.
Mike Stratton & Theresa May. Photo Credit – Sanger Institute, Genome Research Limited.
It is also the site where the UK’s contribution to the original Human Genome Project took place over 15 years ago. The campus is now home to some of the world’s foremost institutes and organisations in genomics. There is now have a real opportunity to turn discoveries about genomics into healthcare benefits for NHS patients. The 100,000 Genomes Project is currently the largest whole genome sequencing initiative of its kind in the world. It aims to harness the potential of whole genome sequencing within routine NHS care.
People currently taking part in the Project are NHS patients with rare diseases and their families, as well as patients with certain common cancers. Those who take part are set to benefit through better diagnoses and personalised treatments.
Scientist working at an Illumina sequencing machine, Ogilvie bulding, Wellcome Genome Campus, Cambridge.
As part of the opening, Sir John Chisholm, Executive Chair of Genomics England was introduced to the Prime Minster along with Dr Dame Bridget Margaret Ogilvie and David Bentley, Vice President and Chief Scientist of Illumina. They then showed her the work going on in the sequencing centre along with Chief Scientist at Genomics England Professor Mark Caulfield and Chief Scientific Officer for NHS England, Professor Sue Hill.
Sir John Chisholm, Executive Chairman of Genomics England said;
The UK is recognised across the world for being the first nation to introduce whole genome sequencing at scale in routine care environments. The Ogilvie facility is central to that achievement and opens the way to the virtuous circle of treating patients with genomic medicine leading to knowledge creation leading to advanced therapies leading to superior health outcomes.
Professor Mark Caulfield, Chief Scientist for Genomics England said;
NHS patients will be the first to benefit from discoveries made from this project. The 100,000 Genomes Project Genome Sequencing Centre has already enabled us to feedback results to participants with rare diseases who had not achieved a diagnosis through routine healthcare
UK Prime Minister Rt Hon Theresa May, said;
It is an honour to open these buildings as they truly represent cutting edge British science and business in the modern era. What I’ve seen on the Wellcome Genome Campus is an excellent example of research from across the UK and around the world coming together with commerce to deliver benefits for everybody including patients in the NHS. We want the UK to be the ‘go to’ place for scientists, innovators, businesses and investors. This really is a very good example of that.
Professor Sue Hill, Chief Scientific Officer for NHS England said;
This collaborative partnership working with the latest sequencing and interpretation technologies will provide improved diagnosis and treatment options for patients; and support research and further learning into how we understand and treat disease.
NHS England is proud to support clinicians in our 13 NHS Genomic Medicine Centres in harnessing this technology for the benefits of their patients, particularly those who suffer from cancer and rare diseases. The 100,000 Genomes Project is putting the NHS at the forefront of genomic medicine internationally, and will form a platform for the wider uptake of personalised medicine approaches in years to come.
Professor Sir Mike Stratton, director of the Wellcome Trust Sanger Institute and chief executive of the Wellcome Genome Campus, said:
Genomes and biodata are an important part of all our futures. The Campus is home to research institutes, spin-out and start-up companies, academic-industry partnerships and Genomics England; all dedicated to driving and leading pioneering research and innovation and discourse in the sphere of genomes and biodata.
The new buildings mark the next major step in the progression of our vision for this Campus as a global hub for genomics and biodata. We have an ambition to translate and commercialise research findings, as well as inform and enable the NHS to integrate genomics into clinical care.
David Bentley, DPhil FMedSci, Vice President and Chief Scientist, Illumina Inc. said;
It was an enormous pleasure to host the Prime Minister, Rt Hon Theresa May MP, and demonstrate the importance of industrial partnership for patient outcomes and sustained change.
With the building of our new headquarters for Europe, Middle East, and Africa at Granta Park, Cambridge, Illumina’s inward investment to the UK is set to continue along with our projects to support the NHS, and we have every confidence in the country’s unique position to be a leader in genomics in the forthcoming revolution in personalised medicine.
Genomics plc, a leading analysis company developing an integrated platform to uncover the relationships between genetic variation and human disease, today announced that it has been appointed as Analysis Partner for the Genomics England Genomics Expert Network for Enterprises (GENE) Consortium. Genomics plc will be analysing genomes at an unprecedented scale and, together with the company’s existing knowledge base, be providing insights into human biology that will help to inform pharmaceutical R&D investment decisions.
Genomics England is delivering the UK 100,000 Genomes Project – whole genome sequencing rare disease and cancer patients in the National Health Service. Genomic information has huge potential to transform drug development pipelines, and one of Genomics England’s four main goals is ‘to enable new scientific discovery and medical insights’. To that end, in 2015, it set up the GENE consortium, which included major pharmaceutical companies such as Abbvie, AstraZeneca, Biogen, GSK, Roche, Takeda and UCB. With a focus on patients with rare diseases and cancers, over 13,000 genomes have already been sequenced and, within its secure IT infrastructure, de-identified data are being made available to Consortium participants to accelerate the development of new diagnostics and treatments for patients.
The power of genomic data to gain novel biological insights grows with both the scale of the data and the breadth of associated physical and biological information. Genomics England’s genetic information is increasingly linked to electronic medical records, a rich source of such phenotypic data, but one that adds many dimensions to the complexity of the analysis challenge.
Understanding and using such datasets to their full potential requires an in-depth understanding of genomics, sophisticated statistical analysis approaches, creative visual representations, computationally efficient algorithmic design, a dedicated IT infrastructure, and an expert team of scientists and IT engineers. Since its formation in early 2014, Genomics plc has been building a powerful platform combining these elements along with a database of genetic and linked phenotypic data on almost 3 million individuals that seamlessly integrates results from over 700 genetic studies across over 500 phenotypes, the largest dataset of its kind in the world. It is also collaborating with major pharmaceutical companies including Biogen, Eisai, Merck and Vertex, as it applies its integrated platform across all areas of pharmaceutical R&D, including target validation, assessment of on-target safety effects and discovery of repositioning opportunities.
Financial terms were not disclosed.
John Colenutt, CEO, Genomics plc, said: “We are excited to be working with Genomics England on the world-leading 100,000 Genomes Project. The use of human genetic data is increasingly recognised as a mechanism to transform productivity within the pharmaceutical and diagnostic research and development industry, and we look forward to working with the GENE Consortium, its members, and others within the sector to improve human health and reduce healthcare’s economic burden.”
Sir John Chisholm, Executive Chair, Genomics England, said: “The potential for genomics to transform healthcare, from better diagnoses to new drugs and treatments, is extraordinary, and we are delighted to work with Genomics plc, a proven leader in the field of genomic analysis, to maximise the value of the 100,000 Genomes Project for patients”.