World of Genomics: England

Best known for fish and chips, football, the Royal Family, and Shakespeare, England is also a world-leader when it comes to genomics research. Being a UK-based company in the genomics field, and having had the opportunity to speak to English leaders in the genomics space at our event “The Festival of Genomics and Biodata”, we know the genomics scene in England pretty well – or so we hope! The UK, and by extension England, is currently positioning itself as a “Genomics Superpower,” so read on to find out more.

The population of England

England is part of the United Kingdom and covers more than half of the island of Great Britain. To the north of England is Scotland and the Irish Sea, to the west lies Wales and the Atlantic Ocean, to the south the English Channel, and to the east the North Sea. England’s geography features rolling hillsides, with mountain ranges including the Pennines to the north.

England has been inhabited for over 800,000 years, as evidenced by stone tools and footprints found in Norfolk. The earliest sign of modern human life in North-western Europe, a jawbone found in Devon, dates back 41-44,000 years ago. England has a rich history of human habitation, with remains from the Mesolithic, Neolithic and Bronze Ages, such as Stonehenge and Avebury. In the Iron Age, Britain was inhabited by the Celtic Britons and in AD 43 the Roman conquest of Britain began and lasted until the 5^th century.

The end of Roman rule led to the Anglo-Saxon settlement of Britain, which is regarded as the origin of England and The Kingdom of England emerged in the 10^th century. In 1066, the Norman conquest of England began a new dynasty. The Tudors and later the Stuart dynasty established England as a colonial power, with the English Civil War resulting in the execution of King Charles I and the establishment of a republic. The British Empire began in the late 1500s in England and ruled the largest colonial empire in recorded history before decolonisation in the 20^th century. In the 19^th century, England became the epicentre of the Industrial Revolution, quickly becoming the world’s most industrialized country.

Geographic and demographic information

Summary statistics

• Land area: 130,278 sq km
• Gross domestic product (GDP):

1. Total: £1.86 trillion (2019)
2. Per capita: £32,866 (2019)

Population statistics

• Population size: 56,536,000 people (2021)
• Birth rate (UK, 2020): 10 per 1,000 people
• Death rate (UK, 2020): 10 per 1,000 people
• Infant mortality rate (UK, 2020): 4 per 1,000 people
• Life expectancy (UK, 2020): 81 years
  • Male 2020 estimate: 79 years
  • Female 2020 estimate: 83 years
• Ethnicities (England and Wales, 2021): White (81.7%), Asian, Asian British (9.3%), Black, Black British, Caribbean or African (4.0%), Mixed, multiple ethnic groups (2.9%), other ethnic group (2.1%)

(Source: Office for National Statistics and World Bank)

Healthcare system

The English healthcare system provides universal healthcare via the National Health Service (NHS) and is funded primarily through general taxation and national insurance. All English residents are entitled to free public health care, including hospital, physician, and mental health care services. The government, through NHS England, oversees and allocates funds to 191 Clinical Commissioning Groups, which govern and pay for care delivery at the local level. Approximately 10.5% of the population in England holds voluntary supplemental insurance for more rapid access to elective care. The government owns hospitals and providers of NHS care, including ambulance services and mental health services, and is responsible for ensuring comprehensive coverage. The NHS provides a wide range of services, including preventive services, hospital care, physician services, mental health care, and rehabilitation.

The main providers of primary care are General Practitioners (GPs), who act as gatekeepers for secondary care. People are required to register with a local GP of their choice, but many practices are full and do not accept new patients, limiting choice. To address the shortage of doctors, there has been a shift towards larger practices using multidisciplinary teams, including specialised services, pharmacists, and social workers. Most GPs are private contractors, but a growing number of practices are employing GPs on a salaried basis. Inpatient specialist care is mostly provided in NHS hospitals, and the NHS reimburses practices for the services they deliver. After-hours care is usually contracted by Clinical Commissioning Groups (CCGs) to GP cooperatives or private companies. Publicly owned hospitals are organized either as NHS trusts or foundation trusts, and all public hospitals have contracts with local CCGs to provide services.

Public Health England (PHE) was a government agency in England responsible for protecting and improving public health. Established in 2013, it combined the functions of several health bodies. On 29 March 2021, the UK government announced that PHE would be disbanded and its functions divided among several organizations. The health protection functions were transferred to the UK Health Security Agency (UKHSA), while health improvement functions went to the Office for Health Improvement and Disparities, NHS England, and NHS Digital (which has now merged with NHS England as of February 1^st, 2023). The UKHSA is an executive agency of the Department of Health and Social Care and is responsible for public health protection and infectious disease control in England, and its establishment was prompted by the COVID-19 pandemic. The formation of the UKHSA took place in 2021 and became fully operational on 1 October 2021.

Healthcare priorities

England has made significant strides in improving public health over the past few decades. Since 1990, life expectancy has increased by over five years for men and over three years for women. The biggest contributor to this rise has been the substantial reduction in cardiovascular disease-related deaths, which is largely due to a combination of declining smoking rates, healthier diets, better access to preventative medication, and improved treatments. The screening of diseases has also been a key focus, with over 21 million tests performed each year covering over 30 conditions. Additionally, vaccination efforts have been successful in reducing the number of cases of infectious diseases, with tuberculosis cases at a record low and HIV diagnoses reaching their lowest levels since 2000.

However, there are still numerous challenges that England faces in terms of public health. The improvement in infant mortality and life expectancy has stalled in recent years, and many people are spending more time in poor health. There is a high prevalence of unhealthy behaviours, such as smoking, that are leading causes of premature death, particularly among low-income and vulnerable groups. Cardiovascular disease remains a major concern, affecting over six million people and accounting for one in four deaths. Additionally, infectious diseases such as measles and sexually-transmitted infections continue to pose a threat to public health.

Despite the challenges, there are also many opportunities for England to continue improving public health. The increasing use of technology, such as online tools and wearable devices, is opening up new avenues for monitoring health, early diagnosis, and tailored advice and support. The focus on preventing cardiovascular disease has been strengthened through the National Cardiovascular Disease Prevention System Leadership Forum (CVDSLF) and local-level efforts to improve detection and management of cardiovascular risk. Moreover, NHS Digital (formerly Public Health England) manages national datasets, publishes tools and resources, and manages disease registries such as the National Cancer Registration and Analysis Service which collects cancer data in England to drive improvements in cancer care and outcomes. The service aims to diagnose 75% of cancers at stage 1 and 2 by 2028 and is working to develop a new indicator to understand the stage at which cancers are diagnosed.

Genomic medicine capabilities

The NHS has a long history in genomics, starting with the first genetic laboratory services in the 1960s and most recently with the launch of the NHS Genomic Medicine Service (GMS) in 2018. The GMS is a nationally coordinated service, locally delivered, that offers cutting-edge benefits for patients, including the use of genomics in routine clinical care. The NHS GMS is the result of a decade of investment in genomics by the UK government and the NHS. The 100,000 Genomes Project, which aimed to sequence 100,000 whole genomes of patients in the NHS, was a big part of this investment. Genomics England was later created to support this effort.

In the UK, there are approximately 300 genetic counsellors – there are approximately 7000 worldwide – and the vast majority of genetic counsellors in England practise within clinical genetics services in the NHS.

The NHS Long Term Plan in 2019 set out that through the NHS GMS, the NHS would use whole genome sequencing as part of routine care for seriously ill children with rare genetic disorders, children with cancer, and adults with rare conditions or specific cancers. The NHS GMS is made up of a consolidated national genomic laboratory network of seven genomic laboratory hubs and seven GMS alliances, a single National Genomic Test Directory, and a clinical genomic service that diagnoses and manages complex rare and inherited diseases. The NHS also has a national genomic knowledge base, a partnership with Genomics England, and a national genomics unit. The NHS has adopted next-generation sequencing panel testing, fetal exome sequencing, and rapid whole exome sequencing. The use of genomic medicine has allowed patients to access over 12 newly licensed precision medicines.

In October 2022, the NHS launched a world-first national genetic testing service that will provide rapid life-saving tests for babies and children. The service will process DNA samples of babies and children who are seriously ill or who are born with rare diseases, such as cancer. It will benefit over 1,000 children in intensive care each year, who previously had to undergo extensive tests with results taking weeks. The service will give medical teams results within days, allowing them to kickstart lifesaving treatment plans for more than 6,000 genetic diseases.

Notable projects

• Genome UK: Government strategy that sets out to “create the most advanced genomic healthcare ecosystem in the world, where government, the NHS, research and technology communities work together to embed the latest advances in patient care.”
• UK Biobank: Established in 2007, the UK Biobank is a biomedical database containing health-related data. This includes genomic data on half a million UK participants.
• Our Future Health: The UK’s “largest ever health research programme”, Our Future Health aims to recruit up to 5 million adult volunteers from across the UK to collect health-related data for research and preventive medicine.
• 100,000 Genomes Project: A British initiative which sequenced 100,000 genomes from approximately 85,000 NHS patients affected by rare diseases or cancer.
• Newborn Genomes Programme: A joint project by NHS England and NHS Improvement (NHSE/I) and Genomics England to sequence the genomes of over 100,000 newborns to identify genetic conditions that can be addressed clinically.
• Cancer 2.0 Initiative: This initiative is comprised of 2 programmes – the Long-Reads and Methylation Sequencing Programme and the Multi-Modal Programme to help clinicians deliver more personalised treatment for 300,000+ patients per year.
• “Data saves lives” strategy: Strategy to make the NHS and social care more data-driven and use data to bring benefits to patients, care users, and staff on the frontline by investing in secure data environments, the latest in technology, and giving people better access to their own data.
• Diverse Data Initiative: This initiative by Genomics England aims to reduce health inequalities and improve genomic medicine by addressing the overrepresentation of populations from ‘WEIRD’ (western, educated, industrialised, rich and democratic) backgrounds in genomic databases.
• National Genomic Research Library (NGRL): A comprehensive database that allows approved researchers access to genomic data, health data and samples, under joint control of NHS England and NHS Improvement (NHSE/I) and Genomics England.

Notable organisations and companies

• NHS Genomic Medicine Service (GMS): The arm of the NHS that harnesses the power of genomic technology and aims to provide equitable care, create a single National Genomic Test Directory which covers the use of all genomic technologies, and create a national genomic knowledge base to provide real world data to researchers and industry.
• Genomics England: A company owned by the Department of Health and Social Care and created to execute the 100,000 genome project. Partners with the NHS to embed genomics into routine healthcare, improve diagnostics and treatment for patients, power researchers with their large genomic database.
• Oxford Nanopore Technologies: Founded in 2005, Oxford Nanopore has developed long-read sequencing technology and is the only company that offers real-time analysis of native DNA or RNA and sequence any length of fragment
• Wellcome Sanger Institute: Established in 1992, a non-profit research organization focused on genomics research. Funded mainly by the Wellcome Trust, it was created to play a role in the Human Genome Project as a major DNA sequencing centre.
• Institute of Cancer Research: Established in 1909, and specialises in genetic epidemiology, molecular pathology, and therapeutic development for cancer research. The ICR is most famous for identifying that the basic cause of cancer is damage to DNA.
• Health Data Research UK (HDRUK): An independent, registered charity which aims to “develop and apply cutting-edge approaches to clinical, biological, genomic and other multi-dimensional health data, addressing the most pressing health research.”
• UK Health Security Agency (UKHSA): Formed after the dissolution of PHE and is responsible for “protecting every member of the community from the impact of infectious diseases” and other health threats.
• Centre for Improving Data Collaboration: A new business unit within NHSX (NHSX is a UK government unit which sets national policy and best practice) which aims to support the NHS and social care to enter into data-sharing partnerships to benefit patients and the public.

Notable individuals

• Francis Crick: English scientist who played a crucial role in deciphering the helical structure of the DNA molecule.
• Rosalind Franklin: English chemist and X-ray crystallographer who played a central role in uncovering the molecular structures of DNA, RNA and viruses.
• Frederick Sanger: English biochemist who won two Nobel Prizes in Chemistry for his ground-breaking discoveries: The molecular structure of proteins, and the development of “Sanger sequencing” which is a chain-terminating method for DNA sequencing.
• C.H. Waddington: A British developmental biologist and geneticist who laid the foundations for systems biology, epigenetics, and evolutionary developmental biology.
• Reginald Punnett: An English geneticist who co-founded the Journal of Genetics with William Bateson in 1910. He is probably best known for creating the Punnett square which is still used by biologists today to predict the probability of possible genotypes of offspring.
• Dame Anne McLaren: An English scientist who was a leading figure in developmental biology and whose work helped lead to human in vitro fertilisation.
• Adam Rutherford: English geneticist, best known for his contributions to the Guardian and popular science books such as “The Book of Humans” and “A Brief History of Everyone Who Ever Lived”.

Future genomics landscape

England already has a strong history of cutting-edge genomics research, and this trend looks set to continue in the coming years. The National Health Service (NHS) in England is currently piloting a potentially revolutionary blood test, known as Galleri, that can detect over 50 types of cancer in its early stages. The test, developed by GRAIL, can detect these cancers through a simple blood sample and will be trialled on 165,000 patients. The results of the study are expected by 2023, and if outcomes are positive, the pilot could be expanded to involve about 1 million participants in 2024 and 2025. The Galleri blood test can detect various cancers that are difficult to diagnose early, such as head and neck, ovarian, pancreatic, oesophageal and blood cancers. The test could help the NHS reach its goal of increasing the proportion of cancers detected early, which is crucial to reducing cancer mortality.

To further realise the potential of genomics data, NHS England and the government’s “Data saves lives” strategy has outlined a plan for improving the use of data in healthcare, with the goal of using genomic data in combination with other health data to drive improvements for patients. The NHS aims to develop an interoperable data infrastructure and use cutting-edge tools to maximize diagnosis and access to precision medicine. The National Genomic Research Library (NGRL) has grown to include over 110,000 clinically linked genomes, making it one of the largest collections of whole genomes in the world for cancer and rare disease research. The recent update, part of the 100,000 Genomes Project, added aggregated data of over 78,000 genomes and allows for easier research using the Genomics England Research Environment platform. Moreover, the constantly improving clinical data from NHS Digital and Public Health England complements the detailed genomic data, making it a valuable resource for disease-specific research.

In December 2022, NHS England announced a £13.5 million investment for the development of a network of secure data environments (SDEs) for health and social care data. These SDEs, which meet high standards of privacy and security, will facilitate research and analysis of health data without compromising privacy. The funding is part of a larger investment of £200 million for making health data more accessible for research and analysis. The sub-national SDEs will cover 5 million citizens each and will operate in conjunction with the national secure data environment, offering privacy-protected access to data.

Another exciting project that looks set to strengthen the genomics landscape in England is Our Future Health. Our Future Health is the “UK’s largest health research programme” aiming to recruit 5 million people to donate their health information to improve disease prevention, detection, and treatment. It will be a secure, encrypted database that only authorized researchers with strict ethical and scientific criteria can access. The program’s goal is to help future generations live in good health for longer.  It is funded by the UK government alongside various research partners and plans to last until 2025. In December 2022, Genomics England announced it will receive £175 million in funding to support its efforts in boosting the accuracy and speed of diagnosis for cancer patients and newborns with rare genetic conditions. The funding will go towards three initiatives, including a Newborn Genomes Programme that will sequence the genomes of up to 100,000 newborns, a cancer programme (Cancer 2.0 Initiative) that will use genomic sequencing and AI to improve diagnosis, and a Diverse Data initiative to tackle health inequalities by increasing the representation of non-European ancestry in genomic research. Another part of Cancer 2.0 is Genomic England’s plans to create the world’s largest cancer research platform, which will collect and analyse vast amounts of cancer-related data and turn it into better treatments for patients. With AI analytics, the platform will merge various data formats from genomics, pathology, and radiology. Currently, Genomics England has 16,000 participants via the 100,000 Genome Project and aims to digitize hundreds of thousands of pathology and radiology images. The platform aims to be running by the end of 2023. These initiatives aim to create the world’s most advanced genomic healthcare system, supported by the latest scientific advancements, patient engagement, workforce development, and industrial growth.