The Genomics England PanelApp – our public crowdsourcing tool for evaluating and sharing rare disease gene panels – has now reached 150 gene panels at version 1 or above. This means that the ‘green genes’ on these panels can be used in the analysis of rare disease genomes in the 100,000 Genomes Project, helping to find a diagnosis for patients and their families.
The gene panels (or lists) are first created by our team of curators. PanelApp then allows gene panels to be reviewed online by clinicians and scientists. This vital community knowledge is used to establish a consensus diagnostic-grade gene panel for each rare disease in the 100,000 Genomes Project.
PanelApp gene panels are dynamic, and they are continuously reviewed and curated as new knowledge arises. Our 150 Version 1+ panel target was reached last week when curators and clinicians got together for our 6th Gene Panel Curation Day at the Wellcome Genome Campus in Hinxton. Some of our recent Version 1 panels include Developmental Glaucoma, Familial pulmonary fibrosis and Epidermolysis bullosa.
Thank you to all our reviewers who have helped us reach this target!
Professor Joanne Hackett joins Genomics England on 18 April 2017 as its new Commercial Director and lead member of the company’s new Commercial Business Committee.
As Commercial Director, Joanne will develop the next phase of Genomics England’s industry engagement strategy by developing, managing and accelerating relationships with commercial organisations − creating opportunities for collaboration both nationally and globally.
Joanne brings a formidable track record of clinical, academic and entrepreneurial success. Training initially in regenerative medicine, she has gone on to create and sell two companies to major multinationals; hold a professorship at the University of Cambridge; and has worked for organisations such as UCLPartners and Cambridge University Health Partners to translate academic research into medical and commercial returns.
Professor Joanne Hackett said: “The relentless pursuit of better health for the patient population is at the heart of Genomics England. I look forward to being part of the journey and plan to work closely with our stakeholders to realise the potential of genomic medicine.”
Sir John Chisholm, Executive Chair at Genomics England said: “We are delighted that Joanne Hackett is joining Genomics England as our new Commercial Director. She will play a pivotal role in accelerating industry engagement to further our goal of developing new diagnostics and treatments, applied in an NHS that is well prepared for a future of genomic medicine. Joanne’s expertise, drive and ambition will help Genomics England to deliver better care and improved outcomes for patients – not just in the UK, but across the world.”
One key aim of the 100,000 Genomes Project is to improve cancer care for NHS patients. Whole genome sequencing in cancer can enable clinicians to choose better treatments and improve
outcomes for patients through personalised medicine.
Circos Plot from our supplementary analysis.
While the Project continues to recruit patients and develop the infrastructure for interpreting genomic data at scale, we are delighted that the first four cancer whole genome analyses from our ‘fast track’ project have been returned to the NHS in 18 working days of patient samples being dispatched to our whole genome sequencing pipeline.
Our ‘fast track’ project aims to provide cancer analyses within a timeframe that will help in clinical decision-making and care. It is a major part of our plans to build a sustainable legacy for cancer whole genome sequencing.
Further work is needed so the pathways for sample processing and data analysis in whole genome sequencing can be fully accredited for diagnostic use. NHS laboratories will now confirm our reported findings with a standard accredited test, before using the information to guide clinical management.
Chief Scientist, Professor Mark Caulfield says:
“During the early stages of our cancer programme, most patients will not see a personal benefit as we develop the tools, processes and systems to analyse genomes at scale. But this first set of fast-track results is very promising and confirms that we can return whole genome analyses in time to provide better outcomes for NHS patients.”
Throughout 2017 and 2018, we will return results for patients in both rare disease and cancer at pace.
Public Health England has announced that Whole Genome Sequencing (WGS) is now being used to identify different strains of tuberculosis (TB).
This is the first time that WGS has been used as a diagnostic solution for managing a disease on this scale anywhere in the world. The technique, developed in conjunction with the University of Oxford, allows faster and more accurate diagnoses, meaning patients can be treated with precisely the right medication more quickly. Where previously it could take up to a month to confirm a diagnosis of TB, confirm the treatment choices and to detect spread between cases, this can now be done in just over a week by Public Health England’s Birmingham laboratory. This slows the spread of the disease and boosts the fight against anti-microbial resistance.
This world first service has been developed in partnership with Genomics England, National Institute for Health Research (NIHR) and Wellcome Trust. The implementation of this technology will contribute to achieving the aims of the 100,000 Genomes Project.
Health Secretary, Jeremy Hunt, said:
“The UK has a proud history of leading the world in science and innovation – this is another global first for our country. These pioneering techniques will change patients’ lives in the NHS as well as being used across the globe to slow the spread of a terrible disease and take the fight to drug resistant infection.”
Professor Mark Caulfield, Chief Scientist at Genomics England, said:
“Genomics England are delighted to fulfil the transformative ambition of the 100,000 Genomes Project infectious disease programme for the NHS by finding a faster, better diagnostic approach for a tuberculosis which is a major infectious disease causing many deaths world-wide.”
Professor Derrick Crook, Director of National Infection Service, Public Health England, said:
“The use of whole genome sequencing to diagnose, detect drug resistance and very accurately type TB is a world first for any disease on this scale. By working closely with our partners, we are now able to use cutting edge science to effectively treat these patients with the right medicines quickly. We are immensely proud of the contribution this makes to the prospects of better treatment of TB globally. This approach will also increasingly be used for many other infectious diseases. Our ambition is to achieve this as quickly as possible so many infections can be better diagnosed and treated.”
The work has been supported by the NIHR Oxford Biomedical Research Centre, a partnership between Oxford University Hospitals NHS Foundation Trust and the University of Oxford to enable clinical research for patient benefit and foster innovation to improve healthcare.
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.”