Month: May 2018

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
Sarcoma
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.