Category: Genomics England

New genomics education and training resources from the Royal College of General Practitioners

Dr Jude Hayward and Dr Imran Rafi are Co-Clinical Champions for the Royal College of General Practitioners’ Genomics in Primary Care Programme. Here, they highlight resources created by RCGP to help general practitioners understand the impact and applications of genomics in primary care. 

Genomics testing is increasing and growing numbers of patients are likely to present to their GP practice, as the gateway to NHS care, with issues and questions relating to themselves or family members. Genomics is already impacting in Primary Care in the fields of cancer and rare disease, altering the management of patients through improving diagnosis, risk prediction, prevention and treatment. The influence of genomics in prescribing and management of infectious disease in primary are potentially just around the corner.

With funding from Health Education England’s Genomics Education Programme, the Royal College of General Practitioners (RCGP) has created educational and training resources to ensure that the workforce of today and the future is equipped to respond to fast-paced developments in genomics. These are based on outputs from the programme’s Primary Care Strategy identifying only those knowledge and skills required by primary care, avoiding overburdening with information. The College has published a four-part webinar series on familial cancer, rare disease, non-invasive prenatal testing (NIPT) and ethics. There is also a three-part podcast series with an introduction from RCGP Chair, Professor Helen Stokes Lampard. Podcast topics include genomics terminology, application of genomics in primary care and ethical, legal and social implications of genomics in primary care, including direct-to-consumer testing and pharmacogenomics.

To learn more, visit the RCGP and Genomics Education Programme websites.

Meet Professor John Mattick, CEO at Genomics England

Professor John Mattick joined Genomics England as its first Chief Executive Officer on 21 May – coming to us from the prestigious Garvan Institute of Medical Research in Australia. Genomics England speaks to its new CEO to discover more.

What first sparked your interest in science?

I had a wonderful science teacher in secondary school, who led me to love the subject. I was something of an aspiring polymath, having studied and done well in English, Mathematics, Science, Latin and French in the Australian equivalent of my GCSEs, and was disappointed that I could not do English and Philosophy along with my Science course at university. I had decided to do Science, rather than an applied course like Medicine or Law, as I thought it would be more interesting, and suit my soul. In any case, I have always maintained my love of literature, language, music and philosophy, and have branched out into history as well.

What made you specialise in genomics?

In second year of my science degree, I did Biochemistry and Genetics, which I embraced. I was fortunate to begin my PhD in 1972, the year in which gene cloning was invented, and to become part of the pioneering generation of molecular biologists. I have always viewed biology more in informational than chemical terms, hence my attraction to genomics, which is molecular genetics writ large. And I was fascinated by the challenge of understanding how 3 billion bases of DNA, just 6 gigabits in informational terms, manages to produce a walking, thinking human from a single cell – surely the most sophisticated information suite in the world, and not to be thought of in primitive terms.

What led you to the clinical side of genomics?

It has been clear to me for many years that genomic information, integrated with clinical and other data, would lie at the centre of the future of both biological discovery and healthcare, and that the clinic and research would fuse into one – with humans, not model organisms, at the centre. It has intrigued me that many colleagues in biomedical research, which has been traditionally focused on molecular and cellular biology, have been slow to fully appreciate the importance of genomics. Indeed, this was my motivation to accept my previous position as the Executive Director of the Garvan Institute, which was on the understanding that I would promote genomics and informatics both in the laboratory and in the clinic. I hope to take this a lot further now, in collaboration with many partners in the UK, which has leads the world.

As the recipient of many awards and honours, what would you say was your biggest achievement?

I think my most important professional achievement has been to be the first to recognise that the human genome is not largely junk, but rather (that the 98.5% that does not code for proteins) specifies a massive hidden layer of regulatory RNAs that organise our development and provides the platform for brain function. This explains many mysteries, including the fact that the human genome contains the same number (20,000) and largely the same repertoire of conventional (protein-coding) genes as simple nematode worms with only 1,000 cells, so the information that produces a human must lie elsewhere. If correct, this is a huge development in the understanding of the human genome. While not everyone yet agrees with me, the evidence is very strong and my thesis is more widely accepted than it once was. The problem is that this is not a simple ‘discovery’ that can be easily validated, but a major change in the way the genomic programming of complex organisms is understood, which runs contrary to the protein-centric conceptual framework that has dominated molecular biology and the textbooks since the 1960s, which has been hard to shift.

Other personal achievements have been the establishment of the Institute for Molecular Bioscience in Brisbane, the model and forerunner of many outstanding institutes that have established that city as a major centre of research and innovation, the Australian Genome Research Facility as a national centre for DNA sequencing and analysis, and later the development of the Garvan Institute as a global leader in clinical genomics. Of course I am also pleased with these, but I was only doing what was needed to be done.

Of course, my biggest personal achievement is three beautiful sons, and a wonderful marriage.

How has the world of genomics changed since you started your career?

The biggest change has been the spectacular development of DNA sequencing technologies over the past two decades, and the associated huge drop in the cost. Sequencing costs will fall even further in the coming years, to the point where it will be cost-effective (if it is not already) to routinely incorporate whole genome analysis into clinical decision systems and the management of health, both individually and systemically. This will accelerate our understanding of human biology, especially in relation to cognitive functions and fragilities that are difficult, if not impossible, to study in model organisms. It will revolutionise healthcare, transforming medicine from the art of crisis response to the science of good health, with massive improvements in the quality and efficiency of the healthcare system. It will also create many opportunities for industry, with flow on effects from all of these developments to national productivity and the national economy. Genomics England is leading the way, which is why I was attracted to come.

If you could give a younger version of you one piece of advice, what would it be?

Make a success of what’s in front of you, but keep looking up to make sure you are going in the right direction. Everyone is different – so follow your own lights while noting what makes others good. If you want to be a great scientist, focus on the big questions and big mysteries – the things that are not explained or just don’t make sense. Bring energy, intelligence, responsibility and integrity to everything you do. Above all, be a decent, thoughtful, kind and generous person. The world will repay you in spades.

If you weren’t a scientist, what would you be?

A writer, I think. I harbour ambitions to do just that and hope to start work on a serious but hopefully entertaining coffee table book.

And finally, what brought you to Genomics England?

Three things…

Firstly − all of the above. It very much feels like my career to date has been preparing me for this role at Genomics England.

Secondly − this is a hugely important moment in medicine. We are at a tipping point that will largely see ‘one-size-fits-all’ approaches to health consigned to the history books – and Genomics England is one of the few organisations that appreciates the scale of the revolution.

And lastly − Genomics England is ideally placed to shape the future of healthcare: to help deliver a new NHS Genomic Medicine Service; to act as a catalyst for ground-breaking research; to accelerate new discoveries into mainstream care; to make the UK the epicentre of global research, innovation and investment in the most important industry in the world; and, ultimately, to change lives for the better.

Genomics England can transform medical research and healthcare – and I will work to realise its vast potential. This is an exciting organisation at a pivotal point in its history – and I’m honoured to be here.

Response to the Prime Minister’s speech on artificial intelligence

Today, Prime Minister Theresa May will announce the Government’s plan to use artificial intelligence to diagnose cancer at earlier stages, which will reduce deaths by around 10% by 2033.

In response, Sir John Chisholm, Chair of Genomics England, said:

The Prime Minister’s commitment to the Life Sciences Strategy and the opportunities it opens for the UK is very welcome. Combining the unique strengths we have in the NHS linked to our world-class science gives us the chance to be global leaders in 4th generation technologies linked to wellness and health.

Data science and the huge advances in computing and clinical technology are already transforming the lives of patients in the UK and across the globe. The scope and scale of the 100,000 Genomes Project, unparalleled anywhere else in the world, has been made possible through the UK’s unique asset − its National Health Service. The NHS, as the single biggest integrated healthcare system in the world, is able to link lifelong healthcare information with whole genome sequencing data. It is a combination that brings benefit to patients whilst also demonstrating the UK’s competitive advantage in enhancing understanding of diseases, and developing products for earlier detection and treatment.

Over 1,300 researchers granted access to the Genomics England Research Environment

  • The number of users with access to the Genomics England Research Environment has more than doubled since our last update in March 2018 – now over 1,300 researchers are working with data from the 100,000 Genomes Project.

The Genomics England Clinical Interpretation Partnership (GeCIP) is an international consortium of researchers, clinicians and trainees, established to improve understanding and practice of clinical genomics, and uncover new medical insights for patients. Over 2,700 people have come together into 42 research groups, known as ‘domains’. These GeCIP domains are either disease-focused or cross-cutting.

The first members of GeCIP were given access to our Research Environment in June 2017 to work on the de-identified data from the 100,000 Genomes Project and test the environment. Since then, the number of users has grown and this week we’re excited to announce that over 1,300 GeCIP researchers now have access to the Research Environment. These researchers are part of 25 GeCIP domains, mainly covering cancer and rare disease:

Cancer Rare Disease Cross-cutting
Colorectal cancer Neurology Quantitative methods, machine learning and functional genomics
Breast cancer Endocrine and metabolism
Lung cancer Hearing and sight
Ovarian cancer Inherited cancer predisposition
Prostate cancer Renal
Cancer of unknown primary Cardiovascular
Glioma Immune disorders
Haematological malignancy Non-malignant haematological and haemostasis disorders
Melanoma Musculoskeletal
Pan-cancer Renal
Renal cell carcinoma
Testicular cancer
Upper gastrointestinal cancer

See a list of approved research projects

GeCIP members currently have access to 44,067 genomes and clinical data for over 60,000 participants. This is already the largest number of whole genomes with associated clinical data anywhere in the world and excitingly, this will continue to grow with each data release as more patients are recruited to the project and more genomes are sequenced.

We have also linked our data to external datasets, such as Health Episode Statistics, Patient Reported Outcome Measures and Mental Health Services Data Set, to create a really rich resource with longitudinal life course follow-up.

All of these data are housed in the Genomics England datacentre and accessed using the Research Environment, a virtual desktop environment with all of the software and tools required to analyse the data. We hope that by providing all of these data to GeCIP members we’ll be able to gain a better understanding of disease, leading to improved diagnosis and treatment for patients.

Dr William Cross (Queen Mary University of London), a member of the Colorectal Cancer GeCIP domain, said:

Essentially I got involved in the [100,000 Genomes] Project as I am interested in trying to make sense of the vast heterogeneity we see in cancer genomes. There have been several projects like the Project (such as The Cancer Genome Atlas), but where this project is truly unique is the all-encompassing whole genome sequencing (WGS) of samples and the inclusion of clinical annotation, which is commonly missing or unavailable in other projects.

The reason WGS is so exciting is that there is a relatively unexplored world in the non-coding regions of the genome. We may very well find new types of colorectal cancer driven by mutations in RNA genes, for instance.

As for the Research Environment, I think the data are very well organised and accessible. We have been given vast resources in the form of the cluster (grid-computer) and I feel that this was a well-conceived and essential part of the project.

Response to Science and Technology Committee Report on Genomics and Genome Editing in the NHS

The House of Commons Science and Technology Committee has today (20 April) published its report on Genomics and Genome Editing in the NHS.

In response, Sir John Chisholm said:

“I welcome the House of Commons Science and Technology Committee Report on Genomics and Genome Editing, published today. The report is a thorough and thoughtful exploration of the tremendous opportunities that genomics offers to the UK – its people, its health service and its economy.

“The Committee also recognises the huge strides that we have made – placing the UK at the leading edge of genomics discovery. As the report stresses, now is the time for the UK to overcome remaining challenges and capitalise on its global leadership − delivering genomic medicine in the NHS, improving patient outcomes and realising economic opportunities across the world.”

Genomics England uses MongoDB to power the data science behind the 100,000 Genomes Project

Genomics England is using data platform MongoDB to power the data science that makes the 100,000 Genomes Project possible. Our partnership with MongoDB allows the processing time for complex queries to be reduced from hours to milliseconds, which means scientists can discover new insights more quickly.

Genomics England, working with the NHS, is sequencing 100,000 genomes from patients with rare diseases and their families, as well as patients with common cancer. On average, 1,000 genomes are sequenced per week, which amounts to around 10 terabytes of data per day. To manage this immense and sensitive data set, Genomics England uses MongoDB Enterprise Advanced.

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

Managing clinical and genomic data at this scale and complexity has presented interesting challenges. That’s why adopting MongoDB has been vital to getting the 100,000 Genomes Project off the ground. It has provided us with great flexibility to store and analyse these complex data sets together. This will ultimately help us to realise the benefits of the Project – delivering better diagnostic approaches for patients and new discoveries for the research community.

MongoDB Enterprise Advanced satisfied these requirements and has been providing Genomics England with data flexibility, performance at scale and security since the project started in 2013.

Ignacio Medina, Head of Computational Biology Lab HPC Service, University of Cambridge, and Head of Bioinformatics Databases at Genomics England has been building many of the applications that sit on top of MongoDB. He said:

MongoDB is performing beautifully for us. From the beginning of the project it’s been fantastic for our developers to build and iterate quickly. Now that the 100,000 Genomes Project is running at scale, MongoDB is also helping us extend that great experience on to the scientists and clinicians who access the data, making it easier and faster for them to find critical insights in the data.

Two of the important projects also utilising MongoDB are Cellbase and OpenCGA (Computational Genomics Analysis). Cellbase is a data warehouse and open API that stores reference genomic data from public resources such as Ensembl, Clinvar, and Uniprot. By relying on MongoDB, Cellbase can typically run sophisticated queries in an average of 40 milliseconds or less, and complex aggregations in less than one second – down from six hours using previous filesystem-based querying and storage. Importantly, it can annotate about 20,000 variants per second, making it compatible with whole genome sequencing data throughput requirements, while also returning a rich set of annotations that helps scientists better understand the data.

OpenCGA aims to provide researchers and clinicians with a high-performance solution for genomic big data processing and analysis, and the platform includes detailed information on genomic material. This means OpenCGA has the ability to process incredibly complex queries based on a huge variety of variables. By using MongoDB, OpenCGA enables researchers to query data in a wide variety of ways, using MongoDB’s secondary indexes – from compound indexes to query data across related attributes, text search facets to efficiently navigate and explore data sets, and sparse indexes to access highly variable data structures.

Dev Ittycheria, President and CEO, MongoDB, concluded:

The 100,000 Genomes Project hits home for me in a very personal way as I recently lost my mother to cancer. I am extremely grateful that so many brilliant people are dedicating their time and energy to this important project. We are honoured that MongoDB is playing an essential role as the underlying data platform to produce data science that is likely to change the lives of millions of people, including someone we may personally know, for the better. This is the kind of project that inspires us to do our best work every day.

Find out more about MongoDB on their website.

Over 500 researchers granted access to the Genomics England Research Environment

• Over 500 researchers have been granted access to the Genomics England Research Environment, enabling them to carry out pioneering research on the 100,000 Genomes Project dataset.

• Genomics England has also adopted the bioinformatics platform Galaxy, providing initial access to students on the MSc in Genomic Medicine course with thousands of genomic analysis tools.

The Genomics England Clinical Interpretation Partnership (GeCIP) is an international consortium of researchers, clinicians and trainees, established to improve understanding and practice of clinical genomics, and uncover new medical insights for patients. Over 2,700 people have come together into 42 research groups, known as ‘domains’. These GeCIP domains are either disease-focused or cross-cutting.

In June 2017 we gave access to our Research Environment, which contains de-identified data from the 100,000 Genomes Project, to a small group of GeCIP members. These members were provided with a subset of data and tasked with testing the environment’s usability and its analysis tools.

Today, we’re excited to announce that over 500 GeCIP researchers, from UK and international institutions, have been granted access to the Genomics England Research Environment. The researchers are part of these 11 GeCIP domains:

Cancer Rare Disease Cross-cutting
Colorectal cancer Neurology Quantitative methods, machine learning and functional genomics
Breast cancer Endocrine and metabolism
Lung cancer Hearing and sight
Ovarian cancer Inherited cancer predisposition
Prostate cancer Renal

These researchers will be able to work on the data in line with the codes of conduct set out in the GeCIP Rules, Publication Policy, publication moratorium, and their approved research proposals. Over the next few months, more GeCIP domains will be granted access to the Research Environment.

Research Environment file structure

One of the new tools we’ve embedded within the Research Environment is the well-known bioinformatics platform, Galaxy. The open-source platform contains over 5,000 tools that enable researchers to run multiple analyses on genomic data (called ‘workflows’) and visualise their results.

Galaxy is currently available to students on the MSc in Genomic Medicine course.

Prof. Mark Caulfield, Chief Scientist at Genomics England said:

The 100,000 Genomes Project now has the largest number of whole genomes with associated clinical data anywhere in the world. With the first set of GeCIP researchers being granted access to this de-identified data, we’re enabling the translation genomic research into direct patient care for years to come.


Human genome pioneer Professor Sir John Sulston dies

Professor Sir John Sulston. Image Credit: Wellcome

The Wellcome Sanger Institute has announced today the death of their founding director and pioneering scientist, Professor Sir John Sulston.

Sir John founded and directed the Sanger Institute, then Sanger Centre, from 1992 to 2000, leading a historic period of genetic discovery. He led the UK’s contribution to the draft Human Genome, a monumental effort that laid the foundations for the research that is transforming healthcare and understanding of disease today.

Professor Mark Caulfield, Chief Scientist at Genomics England said:

John Sulston was an outstanding scientist who created the Sanger Institute. John’s work and leadership in the Human Genome Project has led to major transformations in research and medicine. The 100,000 Genomes Project is one global endeavour that would not be here without his original contribution.

Professor Tim Hubbard, who worked with Sir John on the Human Genome Project, and who is now Head of Genome Analysis at Genomics England said:

John was an inspirational scientist, mentor and friend. Highly principled, he argued for the reference human genome sequence to be freely available to all, to maximise its benefit for humanity. Today’s requirements for scientific data and results to be shared openly have built on that example. The incredible progress in genomics over the last 15 years are a testament to the benefits of this openness.

Related links:

Celebrating International Women’s Day – a blog from Joanne Hackett

As part of the BioIndustry Association’s celebration of International Women’s Day today, Genomics England’s chief commercial officer Professor Joanne Hackett will be joining Dr Jelena Aleksic, founder and chief executive of GeneAdviser, at a networking evening to explore the topic of genomics and data protection.

BIA’s Women in Biotech Networking Evenings were created for attendees to connect with women from across the sector, share success stories and hear from inspirational speakers. Each event explores a different theme, reflecting speakers’ personal career paths as successful innovators in life sciences. As an academic, entrepreneur, investor and yoga instructor, Joanne is delighted to be taking part. Here she explains why. Namaste genomes!

Joanne Hackett

“Genomic medicine has been a major part of my life, both professionally and personally. I have Coeliac Disease which was only diagnosed by sequencing. It may sound dramatic but genomic medicine has saved my life.

As chief commercial officer at Genomics England, I am revolutionising healthcare in the UK.  We have the world’s largest number of whole genomes with associated clinical data which is already transforming patient’s lives as well as the wider healthcare system. We’re already beginning to make a mainstream genomics medicine service a reality in the UK. This year, whole genome sequencing becomes part of routine clinical care. This is the first time this has happened anywhere in the world. I find this absolutely amazing.

Today I would like to celebrate two things – the success of International Women’s Day, and what’s  happening in the UK’s genomics industry; the huge potential and opportunity that’s there. Realising this potential fully demands more as this transformation can only take place with really solid and productive academic and industry partnerships.

My passion is creating collaborations and relentlessly pursuing better health for all – and this is what I do every day. It is now my duty to pay it forward. This is why I mentor and support individuals on the NHS Clinical Entrepreneur Training Programme, NHS Innovation Accelerator, and DigitalHealth.London Accelerator. I think that the time for talking about genomic potential is past. It’s time to talk to business − and forge partnerships on an industrial scale.”

The networking event takes place this evening in London, hosted by Instinctif Partners.

Joanne has been actively involved in clinical research for over 20 years in North America, Europe and the UK. An accomplished entrepreneur, scientist and strategist, she has experience in the execution and management of complex business transactions, as well as broad business development experience in negotiation, execution and management of hundreds of transactions with pharma, biotech, academia and non-profit organisations.

Genomics England appoints global genomics champion as first CEO

Professor John Mattick

Genomics England announces the appointment of its first Chief Executive Officer (CEO) today. Global genomics pioneer Professor John Mattick will join Genomics England in June. He will lead the organisation as work done in the 100,000 Genomes Project provides the foundation for the systems NHS England is mobilising in its ground breaking Genomic Medicine Service.

Sir John Chisholm, Executive Chairman since the foundation of Genomics England in 2013, will hand over executive responsibility to Professor Mattick. Key objectives will be to shape and drive the strategy needed to realise the potential of genomics in the UK, work in partnership with the NHS, build relationships with patients and the public, further genomic discovery, and work with stakeholders across government, academia and industry to deliver lasting value for patients, the public and the economy.

Professor Mattick comes to Genomics England from the Australia-based and globally respected Garvan Institute of Medical Research, which he has led since 2012. Under his stewardship, the Garvan has embedded genomics, bioinformatics and big data at the centre of its research programmes – making the Garvan one of the leading exponents of whole genome sequencing in the world.

Sir John Chisholm said:

“In a very high calibre field, Professor Mattick emerged as the stand-out candidate. He has pioneered whole genome sequencing and overseen the Garvan Institute’s transformation into one of the most respected genomics centres in the world. We were clear from the outset that we would seek the best candidate – irrespective of nationality − to ensure the success of genomic medicine in this country. Professor Mattick is that candidate.”

Throughout his distinguished career, Professor Mattick has championed genome research and the development of national research facilities, for which he was awarded the Order of Australia and the Australian Government Centenary Medal. He has received international recognition for his scientific contributions to understanding the human genome, specifically his work showing that most of the genome is not evolutionary ‘junk’ as previously thought, but rather is devoted to an extensive RNA regulatory system that organises human development.

Most recently he has been awarded the 2011 International Union of Biochemistry and Molecular Biology (IUBMB) Medal, the 2012 Human Genome Organization Chen Award for Distinguished Achievement in Genetic and Genomic Research, and the 2014 University of Texas MD Anderson Cancer Center Bertner Memorial Award for Distinguished Contributions to Cancer Research.

Professor Mattick will continue his academic career while in the UK at the University Of Oxford’s Green Templeton College. He has been elected to a Senior Research Fellowship at the College for one day a week, which will allow him to continue his pioneering genomics work and strengthen links with the UK research community.

Professor John Mattick said:

“Genomics England is leading the world in bringing genomics into the clinic, understanding the genetic components of disease and translating this knowledge into mainstream healthcare. Bringing genomics to the people will revolutionise medical research, vastly improve personal health and transform the quality and efficiency of the healthcare system, not just in the UK but around the world.

“I am honoured to be asked to lead the organisation at such an exciting and important time. I have spent my professional life exploring the human genome and promoting its importance to understanding human biology, which I regard as the great quest of our age. It very much feels like my career to date has been preparing me for this role and it is an opportunity I intend to fully realise − for the benefit of patients, society and the UK economy.”

Reacting to the announcement, Parliamentary Under Secretary of State at the Department of Health and Social Care, Lord O’Shaughnessy, said:

“I am delighted to welcome Professor John Mattick as the new CEO of Genomics England. As a pioneering individual in his field, he will bring a wealth of knowledge to the role and help us to strengthen the UK’s position as world leader in genome medicine.”

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