Month: June 2020

Genomics England launches next-generation research platform central to UK COVID-19 response

British tech company Lifebit and Amazon Web Services to support a dedicated environment for researchers working on COVID-19 vaccines and treatments

Genomics England (GEL) has today launched a next-generation genomic research platform that will play a key role in the research response to COVID-19. This ground-breaking research environment will transform how genomic data is made usable for global biopharma and academic researchers. It will provide world-class patient data security, while enabling the flexibility required for research at the bleeding edge of science.

GEL has partnered with innovative British deep-tech company Lifebit and is using global cloud provider Amazon Web Services (AWS) to power the platform. The immediate focus for the research environment will be on COVID-19 data and analytics. The platform will ultimately also harness the GEL 100,000 Genomes Project data in the fight against cancer and rare diseases.

The launch of this new research environment reflects a new chapter in the role that genomic research can play in collaborative drug discovery and treatment development for the benefit of the health industry. By using AWS’s scalable and secure cloud computing and storage infrastructure in the UK, and then enabling access, analysis and collaboration through Lifebit’s unique technology platform, GEL will unleash the breakthrough potential of researchers around the world. The data stored on the platform will never leave GEL’s highly secure environment but will allow flexible research access to it. Much like the use of apps on a smartphone, researchers will be able to introduce cutting edge analytical tools of their choice, link those tools securely with their in-house data, and conduct research in private workspaces that are audited, protected and controlled by GEL’s strict information governance policies.

Data looked after by Genomics England is stored securely while enabling better analysis by approved researchers – through Lifebit’s platform.

In addition, GEL, in partnership with the GenOMICC consortium, is working with the NHS to deliver whole genome sequencing of up to 20,000 COVID-19 intensive care patients, and up to 15,000 people with mild symptoms. This data will be stored in the AWS UK Region under the control of GEL.

Lifebit’s leading platform will allow researchers to query, analyse and collaborate over these very large sets of genomic and medical data in seconds. Its enhanced functionality and automated tools will speed up researchers’ understanding of the underlying genetic factors that may explain what makes some patients more susceptible to the virus, or more severely ill when infected. Researchers’ findings will help fast-track the development of vaccines and treatments as well as identify those most at risk.

The launch of the new research environment fortifies the UK’s leadership position in genomics, with the aim of enabling global research collaboration, along with mainstreaming genomic medicine in UK healthcare in partnership with the NHS.

Chris Wigley, CEO at Genomics England, said:

This is all about impact for patients in the UK and beyond, who will benefit from GEL’s support for the response to this terrible pandemic. By improving understanding of why some patients have such severe responses to the virus while others have a mild response, GEL is helping to support vaccine and drug development. This will ultimately ensure that the treatment of the UK’s COVID patients is personalised, safer and more effective.

I am incredibly excited that Lifebit and AWS have joined us to launch the next phase of our research capabilities. Speed is of the essence and it has been heartening to see the dedication to getting this new infrastructure stood up as rapidly as possible.  Beyond the immediate focus on COVID-19, the advanced capabilities of the Lifebit and AWS environment will over time allow us to introduce contemporary bioinformatic workflows for researchers in rare disease and cancer research, unlocking the potential for the UK population genomic data to contribute to target discovery, functional genomics and advanced clinical trial design.

The Chair of GEL’s Participant Panel, Jillian Hastings Ward, said:

I am delighted that the introduction of this new technology not only makes my data more secure, but that it also makes it more useful to researchers in academia and industry around the world.  My hope is that this investment in technology is going to increase the impact that personal data is having on research in cancer, rare disease, and also in COVID-19.

John Davies, Head of UKI Healthcare, AWS Public Sector, AWS, said:

We are delighted that Genomics England has selected AWS and our APN partner Lifebit to rapidly deploy their Covid-19 research environment. Using AWS, Genomics England will be able to provide researchers with access to secure, scalable cloud computing resources that will enable them to perform studies to better understand the virus and deliver better outcomes and treatments for NHS patients.

Dr Maria Chatzou Dunford, Lifebit CEO, said:

Genomics England’s groundbreaking Research Environment changes how population genomics is done forever. GEL is widely recognised as the pioneer of population genomics and now they have architected the world’s most cutting-edge Research Environment. As a British company we are honoured to play a central role in this historic initiative and in the UK’s world-leading COVID-19 Research Response.

For the first time, we have managed to combine Fort Knox-grade security for participant data with maximum research flexibility. GEL sets a precedent on how, by using federated technology, research platforms should bring computation to the data, rather than the other way around. Now disparate cohorts of large and sensitive data can be analysed by researchers without copying or moving the data, and true collaboration can happen. Together with our existing federated deployments with big pharma and research institutions, this rings in an end to the era of risky and unnecessary data transfers.

Find out more about the GenOMICC-Genomics England COVID-19 study.

Twenty years on from sequencing the first genome

In this opinion piece, Chris Wigley, CEO of Genomics England, shares his reflections on the 20th anniversary of the first genome to be sequenced.

Not for a century has the world witnessed a pandemic on anything approaching the scale of COVID-19. Millions have been infected, almost half a million have died, economies have been shut down, jobs lost, schools closed, families divided, and civil liberties restricted to levels unknown outside war time. As the UK cautiously tip toes out of lock-down, the virus continues to wreak havoc around the world. While we can manage risk, few believe the scourge will be fully conquered without the development of an effective vaccine.

The search for a vaccine is already underway, with researchers from China, the US and Europe racing against time to deliver a response. Even when such a vaccine is available, however, a crucial factor in combating the virus’ deadly impact will lie in determining those who need it most, those who, for whatever reason, are most at risk. That will not be easy.

COVID-19 is not uniform in its impact. For all too many it has proved deadly yet for others its impact has been negligible. But why? Some correlations are clear, related to factors such as age, underlying health conditions, living standards or ethnicity for example. But for the moment they are just that, correlations – associations, not causes.

The key to cracking the conundrum lies in the science of genomics. Twenty years ago today the multinational Human Genome Project team announced that they had sequenced the human genome. They output was a diagram of every single gene, every letter of DNA within the human body.

It was, rightly, hailed as an amazing breakthrough. Bill Clinton described it as “the most wondrous map ever produced by humankind”. Scientists dreamed of the benefits that would accrue; of treatments for conditions such as cancers, Alzheimer’s, cystic fibrosis. Such treatments could be tailored to individual needs – a kind of made-to-measure medicine.

But much work remained to be done. Each genomic map was unique. What was needed was not one map, but hundreds of thousands, even millions across the world. Such a data base would allow scientists to look for fractional differences between the maps. Groups with genetic differences and  medical conditions in common would suggest an evidential link between the two. The bigger the data base, the more anomalies could be spotted, the stronger the evidence.

In July 2013 the then prime minister, David Cameron, set up Genomics England. The aim was to make more data available to health professionals, academics and others, support their research work and encourage the translation of their results into front line health care. To turn science into healthcare, using technology. One of our flagship projects was to boost the UK data base by sequencing 100,000 whole genomes. In 2018 the target was lifted to 1 million with an ultimate goal of 5 million within five years.

While more data means stronger evidence, it has also increased the importance of being able to effectively mine that data. That requires an alliance of data collection, bioinformatics and advanced analytical techniques like machine learning. But above all it requires the willingness of patients to knowingly and willingly provide the data on which the whole science of genomics rests, and ideally to engage with the research that results.

The arrival of COVID-19 has provided an added spur to our efforts. We are hard at work building up more evidence of what determines the severity of a person’s response to COVID-19. To do that, we need to examine the genomes of folks who respond really badly to the disease, and those who respond unexpectedly well (indeed, may have no symptoms at all), and compare them with the wider population.

In partnership with the NHS, the GenOMICC consortium and Illumina, we are therefore collecting and analysing the data from up to 20,000 patients who needed intensive care treatment as a result of contracting COVID-19 and up to another 15,000 who were either mild responders or asymptomatic.

The work will look at the varied effects of COVID-19 with the aim of identifying those most at risk and helping to fast track new therapies in clinical trials. If you have had COVID-19, either severely enough to be in intensive care, or mildly enough to only have modest if any symptoms – we’re looking for volunteers: go straight to our sign up page.

Twenty years ago, the researchers who manually wove that gargantuan tapestry would have gaped at the idea that we could sequence hundreds, even thousands of genomes at a time, or that those data could in a matter of weeks be available in secure workspaces for researchers around the world. The advances in technology and science, and the reduction in cost and time of sequencing, have powered a revolution over the last couple of decades. COVID-19 is now forcing another evolution, some might say revolution: driving us with ever greater urgency to deliver predictive, prescriptive and personalised health care. To bring the benefits of genomic medicine to everyone.