UK at the forefront of genomics research

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Robert Roe takes a look at genomics research uncovering insights into Covid-19, and paving the way for better cancer treatments

Patients across the UK will benefit from better healthcare, treatments and faster diagnosis as the government sets out plans to deliver genomic healthcare.

Genomics is the study of genetic information and can help diagnose diseases earlier and more accurately, reduce some invasive procedures and enable tailored treatments. Building on the success of the 100,000 Genomes Project, the UK government has committed to sequence one million whole genomes – 500,000 genomes in the NHS and 500,000 in UK Biobank – which will transform healthcare in the UK and create jobs.

In addition, genomics has also been used to better understand Covid-19 and the variants that have increasingly become one of the biggest concerns of the pandemic.

Each variant is made up of a collection of mutations. The majority of mutations don’t change how the virus behaves. However, some mutations can change the properties of the virus, and potentially give rise to a new variant. Many of these ‘mutations of interest’ occur in the spike protein, which is what gives the virus its ability to target, latch onto and enter the cells that it infects.

Working with key partners across the genomics community, the bold new Genome UK implementation plan 2021 to 2022, published in May, sets out 27 commitments to deliver over the next year, including five high-priority actions: faster diagnosis; whole genome sequencing for patients with rare diseases; engagement closely with different communities to ensure diverse datasets; recruitment of up to five million people representative of the UK population; to develop global standards and policies for sharing genomic and related health data.

Faster diagnosis and treatment of cancer using genomics through a partnership between Genomics England and NHS England will help researchers and healthcare professionals identify technologies that could be used to provide faster and more comprehensive genomic testing for cancer.

Whole-genome sequencing for patients with rare diseases and cancer, as part of the NHS Genomic Medicine Service, will build on the success of the 100,000 Genomes Project, and aims to increase the amount of genomic data available to researchers.

The drive for larger and more diverse datasets from different communities aims to ensure that everyone across the UK can benefit from genomic healthcare and genomic databases that are representative of such a diverse population. This is essential for equitable access to new techniques, such as polygenic risk scores (PRS), which compares a person’s risk to others with a different genetic makeup, and pharmacogenomics, which examines the role of the genome in the body’s response to drugs.

Developing global standards and policies for sharing genomic and related health data ensures accurate and quick sharing of research data, which will help to benefit the entire genomics community.

The National Institute for Health Research, Medical Research Council and Wellcome Trust will, over the next five years, provide £4.5m of funding to the Global Alliance for Genomics and Health, ensuring standards are easily accessible and usable by global genomic programmes and data-sharing initiatives, placing the UK at the forefront of secure sharing of international genomic and health-related data.

Matt Hancock, the UK’s Health Secretary, said: ‘We will transform the UK into a life sciences superpower. We’ll build on the success story of our life sciences during the pandemic, which has led the world in everything from vaccine development, to finding effective treatments that work, to genomic sequencing.

‘Today we’ve published our Genome UK implementation plan for how we can build on this even further, including our commitment to sequence one million whole genomes. Because genomics saves lives, and I’m determined the UK stays at the forefront of this vital new technology,’ Hancock continued. ‘If we draw on ingenuity like this, we can keep up the fight against Covid-19, and also tackle the other things that stop us living healthier lives like cancer, dementia and heart disease.

‘So, we’re increasing UK investment in research and development, bringing much more of the supply chain onshore, sparing no effort to attract the brightest innovators and the best manufacturers,’ he concluded.

Minister for Innovation Lord Bethell said: ‘The UK has a proud history in developing genetic and genomic technologies which improve the lives of patients across the country and globally.

‘This implementation plan demonstrates the great strides we have already made since the launch of Genome UK, and outlines the actions we are taking to progress key commitments over the next year.

‘It is vital that we continue to maintain and develop our global leadership in this field, to realise the full potential offered by genomics,’ Lord Bethell added.

This first phase implementation plan follows on from Genome UK: the Future of Healthcare published in 2020, which set out a vision to create the most advanced genomic healthcare system in the world, to deliver better healthcare at lower cost.

Genomics is just one example of the government’s commitment to driving forward health innovation in the UK, which will be central to the future health resilience, the growth of the UK’s life sciences sector and improving patient care.

Chris Wigley, Genomics England CEO, said: ‘Since the days of Darwin, Rosalind Franklin, Crick and Watson, and Fred Sanger, the UK has been at the forefront of genomic science. With this publication it’s exciting to see the next chapter of that story coming to life. Our ecosystem has come together as never before through the difficult times of the pandemic – and this implementation plan will allow us to build on this collaboration between all of the world-leading genomics institutions in the UK.’

Professor Dame Sue Hill, NHS England’s Chief Scientific Officer, said: ‘The NHS is already a global leader in genomics and has introduced a range of new cutting-edge tests for people with rare diseases and cancer over the last year, despite the pandemic.

‘Genomics can truly transform the way patient care is delivered, helping to predict and prevent disease, personalise treatments and ultimately save lives.’

Understanding Covid-19

In February 2021, the UK’s Covid-19 Genomics UK Consortium (COG UK) launched the COG-UK Mutation Explorer (COG-UK-ME) – an interface that provides access to data on Sars-CoV-2 mutations and variants of interest in the COG-UK genome sequence dataset. COG-UK-ME allows anyone to view information about important changes in the Sars-CoV-2 genome over time.

The tool is updated twice weekly, and largely focuses on spike gene mutations of potential or known importance; providing information on cumulative frequency and data for the last 28 days, to give an approximate assessment of recent changes.

COG-UK-ME draws UK genome data from the MRC-CLIMB database. This data visualisation tool allows anyone to follow information over time on important changes in the Sars-CoV-2 genome.

How does COG-UK-ME work?

Selecting the ‘Mutational Explorer’ tab takes you to three tables. Table 1 lists mutations in the spike gene that have led to an amino acid change (called a substitution, which is concentrated on because it may change the way that the virus interacts with humans).

Mutations are ranked by frequency in the MRC-CLIMB database (the most common mutations first). A search function allows individual mutations to be selected, and a file downloaded containing a list of COG-UK identifiers, dates and lineages. For example, selection of E484K provides links to information for each genome that carries this mutation, the date of the sample, and the lineage the isolate belongs to.

Data can also be visualised for each mutation in a graph by clicking the visualiser tab. This shows the number of times the selected mutation has been detected over time.

COG-UK-ME also displays mutations that could affect the way that the virus interacts with the human immune response based on laboratory studies (Antigenic information tab).

Scientific evidence is graded. ‘High confidence’ is applied when a mutation is found by multiple independent studies using multiple different approaches, including studies using polyclonal (convalescent or post-vaccine) antisera; ‘medium confidence’ means this has been found by multiple independent studies; and ‘lower confidence’ indicates this has been found by a single study only. Mutations with an antigenic role can also be filtered by domains of the spike protein.

The Explorer will be updated with new functions over time, based on scientific observations and ways of describing and thinking about variants. The current Covid-19 pandemic, caused by Sars-CoV-2, represents a major threat to health. The Covid-19 Genomics UK (COG-UK) consortium has been created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government.

Led by Professor Sharon Peacock of Cambridge University, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and 12 academic partners providing sequencing and analysis capacity. Professor Peacock is also on a part-time secondment to PHE as director of science, where she focuses on the development of pathogen sequencing through COG-UK.

COG-UK was established in April 2020 supported by £20m funding from the Covid-19 rapid-research-response ‘fighting fund’ from the UK government, and administered by the National Institute for Health Research, UK Research and Innovation and the Wellcome Sanger Institute.

The consortium was also backed by the Department of Health and Social Care’s Testing Innovation Fund in November last year to facilitate the genome sequencing capacity needed to meet the increasing number of Covid-19 cases in the UK over the winter.

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