Category: Genomics England

Tissue Handling in the Royal College of Pathologists Bulletin

A recent article in the Royal College of Pathologists‘ bulletin provides a summary of our recent Tissue Handling Workshop.

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One of the major challenges of the 100,000 Genomes Project has been collecting tissue samples from participants so that DNA can be extracted and sequenced.

Early experiments showed that how the samples are collected, stored and processed can affect the quality of the DNA, and therefore the success of whole genome sequencing, so a new objective emerged: to transform pathology services’ tissue handling practices in the NHS.

How could we better preserve and process tissue samples to make sure DNA remained as intact as possible, giving the highest quality genome sequencing further down the “pipeline”? We know that fresh tissue produces excellent Whole Genome Sequencing results. But, some pathologists hesitate to use refrigeration for fresh tissue sampling in case it affects other diagnostic tests.

However, as set out in this paper by our pathology experts, Professor Louise Jones and Dr Clare Craig, these same changes are seen in samples that are treated in the conventional way, i.e. placed unopened into formalin until they can be batched for sampling.

This is why diagnostic biopsies are used, where possible, in preference to surgical resection samples when immunohistochemistry or other testing that may have a clinical impact is necessary. Dr Craig said:

Thought should be given into the quality of the conventional approach before critiquing the quality of any new approach. Pathologists have a challenge ahead to navigate how best to handle tissues to enable optimal results with respect to morphology, immunohistochemistry and molecular pathology.

In addition to the article, we have sets of videos (available both here on the website and via Vimeo) covering:

  The Tissue Handling Workshop talks
  How to sample different tissue types – for pathologists

These videos have been accredited by the Royal College for Continuing Professional Development (CPD) credits; follow the links to request certificates.

We are also working on a short animation to describe how formalin damages DNA in tissue samples – watch this space for updates.

British Heart Foundation Chief Executive joins the 100,000 Genomes Project

The British Heart Foundation‘s Chief Executive, Simon Gillespie, has recently become a 100,000 Genomes Project participant as a result of his inherited, and unexplained, high cholesterol. He has been speaking about his motivation and expectations this week.

Simon (left) during his initial consultation at Guy’s Hospital, where he was recruited to the Project by Professor Anthony Wierzbicki (not pictured) – image from BHF

Video by the British Heart Foundation

Our Chief Scientist, Professor Mark Caulfield, is a cardiovascular genomics researcher and co-director of the William Harvey Research Institute who has received funding from the BHF for much of his career. He knows better than most that the huge medical potential of the project is matched only by the scale of the task at hand.

The sequencing facility reads through each of the 3.2 billion letters that make up your genome. We read through it looking at the different parts of the genome to see if you carry susceptibility to the disorder that you’ve been enrolled against. Reading through that very carefully we can find answers for around a quarter of the participants in the 100,000 genomes project.

The potential of genomics is endless, leading to more precise diagnostics for earlier diagnosis, new medical devices, faster clinical trials, new drugs and treatments and potentially, in time, new cures. But a more immediate impact will be a long-awaited diagnosis for some participants, enabling their clinicians to make more informed decisions about patient care.
As Professor Caulfield explains:

We get a comprehensive picture of your or my genetic code and that gives us the best chance of getting answers for patients.

Rare cardiovascular conditions are among over 200 disorders that are currently included in the 100,000 Genomes Project. If you have a rare disease or cancer in your family and are interested in taking part, you can find more information here.

With thanks to Simon Gillespie and the BHF.

Genomics England partners with Inivata and Thermo Fisher Scientific

Genomics England partners with Inivata and Thermo Fisher Scientific to unlock the genomic secrets of blood plasma – and improve our understanding of cancer

Genomics England has announced today a new industry collaboration with leading life sciences companies Inivata and Thermo Fisher Scientific to improve understanding of cancer. The pilot project aims to assess the quality of blood plasma samples and explore the potential of liquid biopsy testing to improve disease management and patient outcomes.

Genomics England’s industry partnership is the first step in a larger three-phase pilot that aims to: evaluate the suitability of plasma samples for whole genome sequencing (WGS); assess the technologies available; and provide a proof of concept study using longitudinal samples (samples observed over a long period of time).

This first phase will see Inivata and Thermo Fisher Scientific analyse around 500 plasma samples donated by participants in Genomics England’s 100,000 Genomes Project. As well as determining the suitability of plasma, the study will focus on the use of liquid biopsy technologies to discover the mutations in the human genome that can lead to or demonstrate the presence of cancer.

Genomics England will share results with researchers in the UK and around the world − with the potential to develop less invasive sample collection techniques, more effective monitoring processes and, ultimately, better cancer care.

Joanne Hackett, Chief Commercial Officer at Genomics England, said,

Genomics England aims to translate the UK’s pioneering genomic research into routine care as quickly as possible − cutting the time it takes to turn a groundbreaking discovery into the diagnostics, treatments and medicines that patients need. Our partnership with Inivata and Thermo Fisher Scientific harnesses the expertise of two of the world’s leading genomics companies and will help us to achieve this hugely important goal.

Michael Stocum, Chief Executive Officer of Inivata, said, “As a company with a strong UK heritage, we are delighted to have partnered with the 100,000 Genomes Project − a world-leading initiative which is committed to keeping the UK at the forefront of medical innovation and care. This pilot study will enable us to combine our efforts through the sharing of insights and the assessment of how liquid biopsy products could ultimately transform cancer care within the NHS, saving lives and money.”

Joydeep Goswami, President of Clinical Next Generation Sequencing and Oncology of Thermo Fisher Scientific, said, “We are honoured for the opportunity to work alongside Genomics England in this important effort to better understand cancer using liquid biopsy. We are encouraged by this and other efforts across the globe, such as the Blood Profiling Atlas in Cancer Consortium, that are focused on advancing new testing approaches to help drive better health outcomes in the future.”

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

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.

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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:


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.


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.


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!


  • 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.

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