Almost exactly a year ago, on 16 March 2020, a group of scientists submitted a proposal to the UK Government outlining the COVID-19 Genomics UK Consortium (COG-UK) plan to deliver large scale and rapid virus sequencing capability.
Fast forward to the present day, and the project has delivered whole genome sequencing of the virus on an unmatched scale – with more than 350,000 viruses sequenced at latest count, nearly half of the total sequences uploaded to the global database.
This British success story is due to the determination of the individuals involved. Consortium lead Professor Sharon Peacock and her colleagues did not wait for the proposal to be approved by HMG before they began sequencing, initially at the Wellcome Sanger Institute before expanding to a network of universities from Edinburgh to Exeter. The team also persevered with maintaining a surveillance network throughout the summer, when all the evidence indicated that the virus was behaving in a stable manner with few mutations. The benefits of COG-UK became evident from September, when the identification of the so-called ‘Kent variant’ enabled Governments to understand the sudden acceleration of cases. In hindsight, the £20m investment looks like exceptional value for taxpayer money.
The pandemic has thrust into public consciousness the application of genomics in microbiology. Yet the potential for genomics to help us predict, diagnose, and treat human diseases has long been evident. With heightened awareness and political support, what can be done to capture the momentum around genomics and translate this into routine care in the NHS?
This was the starting point for a roundtable discussion organised by Policy Exchange and supported by AstraZeneca UK. Attended by key players from across the community, the meeting was led by an opening address from Lord Bethell, Minister for Innovation within the Department of Health and Social Care. The conversation focused on the application of this technology for rare diseases and cancer, whilst also touching on the role of preventative genomics in other common diseases.
The strides made in recent genomics projects have given us a strong grounding. Thanks to the legacy of the 100,000 Genomes Project which began in 2012, 1 in 4 patients with rare diseases who were undiagnosed have received a diagnosis for the first time – a remarkable statistic that demonstrates what whole genome sequencing can achieve. And insights from genomic tests are already informing many day-to-day clinical decisions.
Take cancer care. It is now understood that most medicines only benefit a small number of patients in any given cancer type. With support from genomic tests (be they whole genome sequencing or more targeted panel or hotspot testing), the disease is now commonly differentiated based on the mutation status of genes, rather than the location it is found within the body. This new information is helping to move beyond traditional approaches to care, which would have relied upon a patient cycling through various treatments before locating the optimal clinical response.
This onset of precision and personalised therapies is an exciting turning point. Yet for all the case studies and exemplars, the reality is that barriers persist to their widespread adoption in the NHS. Consistent access to genomic and other molecular testing is a core element of this, and work has been underway behind the scenes, with the establishment of a Genomic Medicine Service (GMS) in England, to be supported by a regional system of Seven Genomics Laboratory Hubs and Alliances.
Three overarching considerations came to the fore in our discussion about what the NHS needed to take forward when the GMS formally launches in the coming months.
1. Equitable access for eligible patients
Important decisions still need to be made about how genomics slots within the clinical care pathway, and the guidelines and management that should accompany genomic testing. Of equal importance is ensuring that the services can be accessed consistently across the country. Our roundtable participants shared anecdotal evidence that some clinicians within England do not always feel clear about where to direct tissue samples, and how to best interact with the new Genomic Laboratory Hub structure. Meanwhile, gaps in data recording mean that it is tricky to ascertain how many patients are being referred for cancer tumour testing from each NHS Trust, and to get an overall sense of the demand within the system. This feels at odds with the bold targets set by both the NHS Long-Term Plan and the UK Government – which has set the aspiration for 5 million genomics tests and analyses to be conducted in the UK over the coming years. A new informatics platform from NHS England may go some way to addressing the data gap, but it will be important for this tool to be responsive enough to spot variation and support the appropriate allocation of resources.
Challenges around equity in access are not confined to specialist and secondary care. One participant at our roundtable said it will be essential to invest in upskilling all sections of the healthcare workforce in basic genomic literacy. How can a patient with an undiagnosed rare disease benefit from our world-class sequencing infrastructure, if their local GP is unfamiliar with the technology and referral procedure?
2. Understanding the symbiosis between science research and healthcare delivery
Existing genomic science resources such as the UK Biobank offer unparalleled opportunities for researchers to understand the determinants of disease. As we look to areas of post-Brexit growth, it is important that we capitalise on this base, whilst embracing the blurring of lines between clinical and research activity.
There is an important lesson here for those with policymaking responsibility in remaining attuned to advances in research. For example, incorporating the discoveries of new tests or gene mutations into the Test Directory in a timely fashion would support clinicians to take advantage of these scientific breakthroughs at the first opportunity.
More fundamentally, there should be an acknowledgement that there is still much we do not know about the future applications of research. This will, at points, lead to challenging trade-offs. Can the collection and storage of large volumes of genomic information be justified to the patient (and indeed taxpayer) when the use of this information may be unclear? And would collecting the polygenic risk scores of healthy individuals reduce or increase the burden on the NHS? These are ongoing discussions in the community – typified by the debate regarding genome sequencing at birth. It was notable that the Government struck a note of caution in its recent 10-year strategy Genome UK, in outlining both the benefits and reservations. At its core, genomic research is a story about health data management and ensuring that patient choice, trust, and consent is maintained.
3. Achieving the balance between optimism and realism
The onset of genomic medicine within the NHS is undoubtedly captivating. But several of the roundtable attendees underlined that we should resist the temptation to be drawn into the vision without adequate recognition of the issues and contradictions that genomic medicine will bring.We know, for example, that overall only 27% of what influences the development of breast cancer is heritable genetic factors, and only a small portion of cases can be linked to a specific predisposing gene mutation (such as BRACA1), meaning that most cases arise predominantly from other factors throughout life. Relying on risk profiling through genomics alone only provides one part of the picture. By the same token, the current evidence suggests that tumour genomic testing can deliver clinically actionable results in more advanced cancers (known as metastatic) whereas the cost-effectiveness of their use in early cancer is less conclusive.
A level-headed assessment of what the technology can and cannot provide applies to rare diseases, too. Achieving a diagnosis represents an important moment for the individual, but it must be accompanied by concerted effort from various partners to unlock and accelerate new treatment possibilities for these patients. This includes rethinking medical research – for example accepting that the process for a regulator to assess a medicine should become more iterative, whereby patient benefit and evidence accumulation go hand in hand.
Conclusion
Much of the hard work of embedding genomics in the NHS – in training staff, formalising new regional structures, and in patient engagement, is still to come. And tackling this holistically will require new types of partnership, between the NHGS Government, research bodies, charities, and pharma.
It will also require foresight planning, and the prudent use of resources given the constrains facing the NHS and wider economy as we emerge from the pandemic. Difficult choices on healthcare spending lie on the horizon, and it is important that Ministers both present and future continue to back this sector as their predecessors have done.
The UK’s heritage in genomic science, as shown by the experience of the COG-UK consortium, combined with the strength of a coordinated NHS means that we are better placed than most to grasp this opportunity.