Month: July 2017

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