News

Helping apprentices lead the field in big data

Anglia Ruskin and Wellcome Trust Sanger Institute team up to deliver new training

Anglia Ruskin University and the Wellcome Trust Sanger Institute have received funding from the Higher Education Funding Council for England (HEFCE) to launch a new degree apprenticeship in Data Science in September 2018.

Anglia Ruskin has been supported in its application by several global companies involved in genetics and computational biology, including Genomics England, as well as Congenica, Eagle Genomics, GlaxoSmithKline, Global Gene Corp, SciBite, and Specific Techologies.

The emergence of big data and its use in biological research has led to a growing need for skilled professionals who can analyse and interpret biological data.
Genomics in particular is a growth industry, with Deloitte reporting that the industry will grow by 20% this year. The degree apprenticeship aims to enable employers to provide in-work training for their employees, improving their skills base and helping to address the shortage of skilled professionals in the “big data” sector.

Dr Augusto Rendon, Director of Bioinformatics here at Genomics England, said:

There is a clear industry and academic need for developing the talent pool of data scientists and bioinformaticians… A key benefit of a degree structured in this way is that it increases the breadth of potential applicants rather than relying on the traditional route of a masters qualification for biology or quantitative science graduates.

The students on this programme will acquire a greater depth of knowledge in areas such as genetics, genomics, coding and data analysis; providing a sound platform for a career in the bioinformatics field.

Janet Scotcher, Director of Human Resources and Organisational Development at the Sanger Institute, said:

This area of work is a relatively new occupation and as such, may not be visible to many young people at the beginning of their careers. Already we are seeing a skills shortage in this important area, despite being acutely aware that genomics and biodata offer an incredibly diverse and promising career path for anyone.

We hope this apprenticeship will help people in search of a rewarding career find an inspiring and fulfilling future.”

For further information, contact degreesatwork@anglia.ac.uk

Wellcome Trust Sanger Institute

The Wellcome Trust Sanger Institute is one of the world’s leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease.

Read More

Genomics England Responds to Report from Life Sciences Sector

In response to a report by Sir John Bell to the UK government, Sir John Chisholm, Executive Chair of Genomics England said:

“Genomics England welcomes Sir John Bell’s report to government from the life sciences sector – recognising as it does the critical role that genomics will play in the future health, well-being and economic prosperity of this country.

The UK has been quick to act on the opportunities of genomics, with significant investment in the 100,000 Genomes Project – harnessing the world’s biggest integrated healthcare system to deliver the world’s largest national sequencing project. Today’s report gives us the blueprint to build on our global lead in genomic science to drive NHS transformation, improve health outcomes and realise material economic benefits for UK plc.”

GENE Consortium legacy steers industry cooperation at Genomics England

On 26 March 2015, Genomics England launched a groundbreaking collaboration with academia, NHS Genomics Medicine Centres (GMCs) and the biomedical and pharmaceutical industries. Known as the Genetics Expert Network for Enterprises (GENE) Consortium, its goals have been ambitious – to align the needs of all sectors to ensure that genomics discoveries are translated into medical treatments, and embedded into mainstream NHS care, as quickly as possible.

GENE has involved 13 private companies working pre-competitively with Genomics England. Originally envisioned as a year-long programme, it has evolved alongside the 100,000 Genomes Project and is now drawing to a close after two years of engagement. GENE has generated a wealth of understanding around how these sectors can collaborate more efficiently – and deliver more effective care.

Photo of Joanne Hackett

Prof. Joanne Hackett

Since starting at Genomics England in April this year, it has struck me that one of the most innovative aspects of GENE was its capacity to remove the barriers between academia, industry, government and the NHS. Breaking these silos helps us to better understand the processes needed to turn pioneering discoveries into practical treatments that can be rapidly adopted in routine care. It is both forging new ways of working and identifying where partnership can be improved.

GENE’s value has focused around key themes:

Collaboration

In bringing together organisations with a diverse set of interests, GENE has allowed participants to identify shared interests and concerns. In addition, GENE has acted as a bridge between researchers, the NHS and industry – pooling expertise, fostering understanding and focusing effort.

Contribution

Many scientific research projects introduce industry late in the development process. This can lead to missed opportunities, such as concentrating efforts on the rapid development of new treatments and medicines. The GENE Consortium has embedded industry at the very start of the 100,000 Genomes Project − early engagement has allowed industry to provide advice and feedback, which has helped to steer the direction of the project.

Value

Industry contributions include identifying aspects of the project that will deliver a return on public investment – i.e. the knowledge base that the project is generating. In better understanding this, Genomics England is looking at the economic – as well as health − benefits that genomic medicine can bring to the UK.  In providing industry with a mechanism through which it engages with genomics research, it is also helping to establish the UK as an attractive place for this research.

Patients and industry

research commissioned as part of the ‘Genomics Conversation’ in 2016 showed mixed results in terms of patients’ attitudes to industry involvement in the Project. GENE has provided an opportunity to explore public perceptions of industry involvement in the Project specifically, and medicines/treatment development more generally − and how it can work to address them and build trust.

As well as areas where collaboration is working well, GENE has helped Genomics England to see where improvements can be made. Industry members identified, amongst other aspects, the need for: a clearer industry focus; further enhancement of the analysis platform; the inclusion of researchers from the Genomics England Clinical Interpretation Partnerships (GeCIPs); and a greater emphasis on patient recruitment and engagement.

Although GENE is now coming to an end, participants are keen that a successor body is established to strengthen collaborative working on the 100,000 Genomes Project. Genomics England is working with members to scope out this new collaborative forum – learning from and building on the legacy of the GENE Consortium.

– Professor Joanne Hackett


GENE Consortium launch (2015)

Genomics England’s GeCIP virtual Research Environment comes online

The 100,000 Genomes Project’s primary goal is to transform the NHS: embedding genomic medicine for earlier diagnosis and more effective treatments. At the same time, the Project is tasked with making the resulting data available to researchers across the world to better interpret genomic data − leading to improved clinical understanding and patient outcomes.

In mid June, we took a big step towards achieving our research goals, with the first groups of scientists accessing data from the Project’s main programme. These research groups form domains known as the Genomics England Clinical Interpretation Partnership (GeCIP). This initial phase brings in 34 researchers from three domains; two disease focused: neurology and colorectal cancer, and one “cross-cutting”: Machine Learning. See the infographic below for details:

A pre-GeCIP group of researchers have already begun working on separate batches of data from the Project’s Pilot phase: on Chronic Lymphocytic Leukaemia or CLL, led by Professor Anna Shuh, and Rare Disease, led by Genomics England.

The Research Environment

Work on this scale has never been attempted before and we need to learn how best to interact with the data. So, we’ve populated our initial learning environment with a subset of data from the cancer and rare disease arms of the Project, comprising 1,207 individuals. The first researchers are helping us test the suitability of the environment, before we scale up access to researchers to a much bigger data resource in the near future.

Just like in a clean laboratory area, researchers must use our virtual airlock, similar to this clean pass-box, to make sure everything coming in and going out is authorised and secure.

One of the biggest challenges in our GeCIP work has been to create systems that give access to researchers, while also ensuring the safety and security of participants’ data, so Genomics England has had to build a unique solution from the ground up.

This solution is an ‘airlock’ between the data and the outside world. Think of the data repository as a huge sterile laboratory: researchers wishing to access it go through the airlock, which ensures that they and the tools they wish to use are properly authorised. Once cleared, they can enter and work on the data, but ‘sealed off’ from the outside world. When they wish to leave, they go back through the airlock, which ensures that what they take out is similarly appropriate and authorised. To protect participants’ data, only analysis results can be taken out – not the individual-level data itself.

In effect, we have created a completely new, virtual and globally accessible Research Environment. It is designed to evolve – embracing as yet unknown tools and techniques – with our growing understanding of the power of genomic medicine. Underpinning everything, however, is our obligation of trust: ensuring that 100,000 Genomes Project participants’ data is always safe and secure.

The opening of this virtual space to the GeCIP is a significant step and I would like to thank everyone for investing their time, patience and commitment to make this work. I know that this global collaboration – bringing together the best minds in genomic research − will deliver real advances in genomic medicine and greatly improved patient outcomes.

– Professor Mark Caulfield


Read the official GeCIP newsletter ‘onboarding’ announcement

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.

1 2 3 4 5 6 9