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The National Initiatives Meeting – genomics around the globe

Three years after the launch of the Global Alliance for Genomics and Health (GA4GH) and six months after the first GA4GH-hosted convention of national genomics initiatives, Kathryn North (Australian Genomics) and Genomics England’s Chief Scientist, Professor Mark Caulfield recently convened representatives from 13 National Initiatives in genomic data collection to discuss areas of potential collaboration at the Wellcome Trust in London.

Genomics England logo

The goal of the meeting was to identify potential areas of collaboration, resource and expertise sharing, as well as common needs across National Initiatives that GA4GH can incorporate into its “toolbox” of data sharing standards and tools.

The meeting was attended by representatives of major population-sequencing endeavours, from: Australia, Brazil, Canada, Finland, GenomeAsia100k, Global Gene Corp (India), the Netherlands, Qatar, South Africa, Switzerland, Turkey, the USA and the UK.

The three more established projects – Genomics England, Australia and the USA gave detailed talks about progress to date and challenges they have faced. This was followed by presentations from all of the emerging projects – covering their aims, funding models, disease focus, and resources they’ve developed. There were also workshops on Data & Sharing, Regulation, and Clinical & Education, as well as a round-table discussion.

Sir John Chisholm​, Executive Chair of the Genomics England Board, spoke on his vision for genomic research:

We are all engaged in the most significant program of the human race in the 21st century. If we’re successful, we’ll change the human experience from what it had been throughout history and evolution—that health is something which gets done to you by some force outside of you—to something you have control over.

This change is possible because we will soon be able to understand the genome, and to use it to predict outcomes.

“It’s a fantastic vision, but it’s very hard and it will take most of rest of the century to get there,” said Chisholm. He cited two challenges in particular:

1. Genomic medicine involves “colossal” amounts—millions, tens of millions, or even 100s of millions—of data points. This scale is necessary because of the low probability of making connections between the genome and human health.

Additionally, because very few associations are monogenic, combinatorial problems make unpacking the genome a very difficult and complex pursuit. In the past, scientific programs have built individual research cohorts for each study. This will not work with clinical genomic research, because no organization has enough money to fund research cohorts at this scale.

The only way to achieve cohorts of the size needed is by aligning fully consented patient data from the healthcare system with genomic data. No one country will be able to do this alone so national programs must collaborate.

Given that no one country can do it alone, nations must agree on rigorous standards and protocols, as artefacts of non-harmonized data collection processes will make it impossible to understand outcomes across a combined data set.

2. Implementing standards and protocols in routine healthcare will be difficult, Chisholm said, “but it’s something where the prize is so great, it’s worth doing.” In the four years since it was launched, Genomics England has spent considerable effort and made progress on the development of standards and protocols for data collection and getting them implemented across the UK’s National Health Service.

Now, he said, that needs to be taken to the international stage. He invited meeting attendees to “form a club” to work together to agree on standards and protocols for clinical genomic data sharing. This will allow for federated data sharing that is protective of participant confidentiality and privacy and enables “this transformation of the human experience in the 21st century.


In closing remarks, Professor Mark Caulfield said that the groups present must showcase their achievements to patients and the public in order to promote further involvement from those communities. Doing so, he said will result in “more ‘Denmarks’ and less places where we lock data away.”

He also summarised a number of high level themes emerging from the meeting:

  • In three years, the discussion has moved from a focus on future goals to examples of established infrastructure and large-scale genomic data collection in health care systems around the world
  • The next step is to position healthcare against research in order to achieve the needed scale, and to move from cohorts of 1 million individuals to 5 or 10 million thanks to shared data across the globe
  • This will require an ethical framework and robust guidelines for follow up
  • Initiatives must engage with patient advocacy and support groups since those populations are willing to take on challenges that researchers shirk from
  • Industry is vital to this endeavor, as it requires millions (or billions) of dollars
  • There is a need for robust IP that allows for freedom to operate, and the ability to account for situations where the responsible act is not to protect IP but to give it away

Project Milestones for our Genomic Medicine Centres

This month we’ve been celebrating four milestones for our brilliant recruitment teams across the country. The 100,000 Genomes Project could not exist without all the hard work of multi-disciplinary teams on the front line in the clinic, who speak to patients about the project and sign them up to be involved as participants.

NHS England established the Genomic Medicine Centres (GMCs) and clinicians based in those areas are working hard to find more people eligible to join the project.

Congratulations to the following GMCs that recently achieved these incredible numbers!

Christine Mather, aged 72, former Medical Director’s PA from Sale, was asked to take part in the project as she was suffering from polycystic kidney disease (also known as ADPKD). She was happy to give a blood sample as she understood that it may help others with the same condition especially as it is known to be inherited. She said:

I don’t want my daughter to have to go through the problems that I have. As soon as they find a cure it will be very good for future generations of my family as well as everybody who has it.

Christine is a patient at Dr Grahame Wood’s specialist ADPKD clinic at Salford Royal, and he said that recent trials have given great hope that new treatments for ADPKD can slow or even reverse this usually progressive disease.

Toby Williamson was born after a normal pregnancy, but it soon became apparent that he was not feeding well, was sleepy and passive and had poor eye control. Tests established that he had abnormally low muscle tone with global developmental delay leading to a visual impairment and severe learning difficulties which means his communication skills are very limited and all non-verbal. His mum, Charlotte, said:

He has the learning age of about a nine-month-old and the physical ability of just over a one-year-old. He relies on us totally for all of his personal care and all of his needs have to be met you have to constantly listen out for him, be aware of things for him.

Toby’s subsequent medical history has included regular ear infections and burst ear drums (upsetting his hearing, balance and learning); reflux, leading to hospitalisation for dehydration and subsequent medication; a squint, corrected by surgery in 2004; a diagnosis of Autism Spectrum Disorder in 2010; and many genetic tests – none of which have yet found a cause for his condition.

For years Holly and her husband were told that Antony, now aged 8 was born with global development delay, and suffered from challenging behaviour that he would grow out of. Three years ago the family were told he suffers with autism, but although the findings were a “relief” there’s still more the family want to know. Holly, who now cares for him full time, said:

Any results could make a big difference to his future, and even if there’s some result, no matter how big or small, it would be great news for us.

The Wessex NHS GMC serves 3.5 million people from Dorset, Wiltshire, Hampshire, Isle of Wight and parts of Somerset, Surrey and Sussex. Every sample collected can ultimately contribute to a report that will go back to a participant and their family, and the wider research effort that will use the huge datasets generated from sequencing samples’ genomes.

Thank you for all your hard work, and to all our participants who’ve signed up so far!


Resources:

  • Consent – for healthcare professionals and participants
  • Results – what can participants find out?
  • Research – joining the research community in the Genomics England Clinical Interpretation Partnership (GeCIP)

PanelApp reaches 150 diagnostic-grade gene panels

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 GlaucomaFamilial pulmonary fibrosis and Epidermolysis bullosa.

Thank you to all our reviewers who have helped us reach this target!

To find out more about our gene panel curation, visit PanelApp.

Professor Joanne Hackett joins Genomics England as new Commercial Director

Photo of Joanne HackettProfessor 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.”

Whole genome analyses for cancer returned to the NHS within three weeks

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

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.

Click here to view an example of our cancer whole genome analyses.

Further information about how genomics can improve understanding of cancer, and how the 100,000 Genomes Project cancer programme works.

Whole Genome Sequencing to diagnose TB

Public Health England has announced that Whole Genome Sequencing (WGS) is now being used to identify different strains of tuberculosis (TB).

Public Health England logoThis 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.

Read more on the Public Health England website.

Rare disease day at London North West Healthcare

Staff at Northwick Park HospitalThe 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.

Scotland study to probe causes of rare diseases

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.

computer filesUsing 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.

Scientist working at a sequencing machineThe 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.”

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.

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.

Find out more:

The University of Edinburgh

The Scottish Genomes Partnership

Announcement of Scottish Genomes Partnership investment

Rare Disease Day 2017

Today (February 28th) is Rare Disease Day.

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.”

Results will continue to be returned throughout 2017 and 2018. Visit our taking part section to find out more about results.

Check out this animation on how we analyse genomes.

More information

Jessica’s Story

Genome sequencing gave Jessica, aged 4, a diagnosis for her rare condition. Find out how.

Rare Disease Genomics

Why do changes in DNA cause rare disease? Learn more about DNA, sequencing and genomics.

The 100,000 Genomes Project Update

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 a sequencing machine

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.

Video

Video

Find out more about the Project in our new video.

Resources

Resources

Browse more resources and videos about genomics.

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