Month: July 2019

Over 100,000 whole genome sequences now available for approved researchers

Data Release 7 has now gone live in Genomic England’s Research Environment. While every data release is significant in its own right, v.7 is symbolic. It means we have now passed the milestone of 100,000 whole genomes available to researchers. Of course it’s not just about genomes. The growing wealth of linked clinical and secondary health data associated with the genomic data in each release is what makes the Genomics England dataset one of the most exciting tools in the world for discovery and translational research.

Speaking on the importance of this release, Genomics England Chair Jon Symonds CBE, said:

The completion of the sequencing of the 100,000 Genomes Project in December was a major accomplishment, representing a tremendous effort across Genomics England and the NHS. Today, we are proud to announce that over 100,000 genomes are now available to researchers through our secure Research Environment. While our priority remains the return of results to participants, this milestone is representative of our commitment to improving patient outcomes through research. By generously consenting to allow their data to be used for research, participants are ensuring that future generations will benefit from the resulting healthcare technologies and treatments that will be made possible by the Genomics England research dataset.

Improvement of patient outcomes through precision medicine technologies is a long-term goal but in fact, researchers accessing the Genomic England Research Environment have already created impact for project participants. To date, there have been 94 researcher-identified potential diagnoses in addition to over 90,000 results returned to the NHS by the team at Genomics England.

Commenting on the research opportunity, interim Chief Executive Professor Sir Mark Caulfield, commented:

Through the Genomics England Clinical Interpretation Partnership and Discovery Forum, great progress is being made in understanding how this dataset can be used to advance scientific discovery and the development of new technologies. Genomics, and improving healthcare, is a global endeavour. As such we are proud to see public and private researchers from around the world recognising the opportunity our Research Environment presents. Their work helps us fulfil our commitment to project participants who want to see their data used to benefit patients globally.

To tell the story behind the numbers, we put a few questions to Dr James Holman, Research Environment Project Lead.

Dr James Holman

What is the significance of this data release and why?

It took a tremendous effort, across the NHS and Genomics England, to recruit thousands of participants and sequence over 100,000 genomes. Alongside that effort, Genomics England has been working hard to make those genomes available to researchers in our Research Environment. This release is a major milestone as it sees us exceed 100,000 genomes. It certainly hasn’t been a trivial exercise, and illustrates the commitment of Genomics England to accelerating scientific discovery. We owe particular thanks to the participants who have taken part in this endeavour.

It shouldn’t be forgotten that, although this one is symbolically significant, every data release has been important. Each release increases the richness of the linked clinical and secondary health data available to researchers, making our dataset a more powerful tool for discovery and translation. Similarly, following data releases will be just as important as we continue to enrich the Research Environment.

That being said, reaching 100,000 genomes in this data release is a significant achievement for the Genomics England Research Environment.

Can you provide a run through of what goes into a data releases and why they take time to prepare?

Each data release is a huge team effort across Genomics England. Together the teams collate, query, and generate data from numerous information systems across Genomics England and integrate them into a unified data release. These data are curated and made available in the various tools available within the Research Environment. That includes existing tools such as our Data Repository, and soon to be released applications such as the Data Discovery Portal and Genomics Analytics Platform.

Before the release goes live, we undertake an extensive review to confirm the integrity of the data and update the data dictionary. We then prepare a data release note to make users of the Genomics England Research Environment aware of what has been added or changed, making sure that we explain any new data features.

What’s coming up for the research environment for the rest of this year and what is your approach to development?

I am in the fortunate position of leading a team that is responsible for delivering innovative solutions to maximise the research potential of the data that’s available. In the coming months we will be delivering a range of new applications that will help researchers discover, understand, and use the data available within the Research Environment. We plan to deliver applications as advanced prototypes and then iteratively develop them based on user feedback. For each type of application released we are using surveys, pre- and post-release, to ensure the tools have the desired impact. This feedback will ensure that they meet the user needs and allow us to deliver value incrementally and continuously based on those needs.

Tools that we are currently testing and preparing for roll-out include a Data Discovery Portal, Terminology Service, OpenTargets, and a genomics analytics platform. We are also undertaking an evaluation of the common data model developed through the Observational Medical Outcomes Partnership (OMOP) Project to determine how suitable the model is for genomic analysis and what extensions may be required.

Chris Wigley appointed CEO of Genomics England

Genomics England has today announced the appointment of Chris Wigley as Chief Executive Officer, with effect from 1 October.

Chris joins Genomics England from QuantumBlack, a world leader in machine learning and artificial intelligence. Machine learning is critical in the analysis of the vast amounts of data involved in genomics, so Chris’ expertise in this area will be invaluable in driving Genomics England’s pioneering work with the NHS to realise the true potential of genomic medicine.

Chris was a Partner at McKinsey from 2009 to 2015. He then focused on growing QuantumBlack, a McKinsey company, as Chief Operating Officer. Prior to this, he worked with the British Foreign Office as a diplomat, and on digital transformation at the BBC.

The Chair of Genomics England, Jonathan Symonds CBE, said:

Chris joins us at a significant time for Genomics England as it takes the next steps in using the data entrusted to us by participants to transform healthcare.  Chris’ vision and energy will maintain Genomics England’s place as a world leader in genomic medicine. His leadership experience at QuantumBlack will be fundamental to our goal of building a world leading organisation delivering genomic science and analytics into routine medical care with our partners in the NHS and medical research.

Chris said:

I am tremendously excited to be joining Genomics England at this pivotal time. The fantastic work on the original 100,000 Genomes Project mission (which many thought was impossible just a few short years ago) shows the talent and grit in this team. Of course it would also have not been made possible without the cooperation of so many stakeholders and, most importantly, the participants who put their trust in the Project and to whom we are deeply committed.  Today, Genomics England’s partnership with the NHS is leading the world in bringing cutting-edge genomics research and analytics into daily medical care to benefit people across the UK and beyond. I can’t wait to join the team and help shape the next chapter in this extraordinary journey to bring digital technologies and products to clinicians and researchers and – most importantly – achieve transformative outcomes for patients.

Sir Mark Caulfield, who has acted as Interim CEO, will continue his excellent strategic scientific and clinical leadership as Chief Scientist in the next phase of transformation of genomic medicine in the NHS.

Jonathan Symonds said:

I would like to thank our Chief Scientist, Sir Mark Caulfield, who acted as interim CEO over the past six months. His leadership as Chief Scientist and commitment to delivering the 100,000 Genomes Project is respected around the world. Mark’s extraordinary contribution to genomics was recognised this year with a knighthood.

Matt Hancock, Secretary of State for Health and Social Care, said:

Genomics has huge potential to diagnose diseases earlier, unlock solutions for rare conditions and provide tailored treatments to individual patients to boost their chances of recovery. It could also help us drive the preventative agenda and help people avoid developing some diseases at all.

“We’re already leading the world in this exciting field and I’m delighted Chris will be helping us achieve our Long Term Plan ambition of bringing the benefits of personalised medicine to every patient, clinician and carer. Chris is a truly transformational leader and I have every confidence he will help the country realise our ambitious, world leading vision for Genomics England.

Baroness Blackwood, Parliamentary Under Secretary of State, said:

I want to personally congratulate Chris on his appointment as Chief Executive of Genomics England. He is an excellent leader with a proven track record of delivery, and I am very confident that Genomics England will go from strength to strength under his leadership. I want to also put on record my thanks to Sir Mark Caulfield for his work as interim CEO over the past six months. He has made a fantastic contribution to genomics over his career and I am very pleased that this was recognised with a knighthood in the Queen’s Birthday Honours.

Lord Prior, the chair of NHS England, said:

We are delighted that Chris Wigley will join Genomics England as Chief Executive. He has huge experience in digital innovation technological transformation and data analytics. His leadership and vision will bring exciting opportunities for Genomics England as it works hand in hand with the NHS to introduce personalised, precision medicines, early diagnostics and targeted prevention.