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Genomics strategy and implementation in the NHS in England
The document outlines the UK's Genomic Healthcare Strategy, titled 'Genome UK', aiming to enhance genomic medicine within the NHS over the next decade. It highlights key themes such as embedding genomics into the healthcare system, delivering equitable genomic testing, and integrating genomic data with cutting-edge technology to improve patient outcomes. Challenges noted include costs of genomic testing, workforce development, and ensuring public engagement and education in genomics.
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Genomics strategy and implementation in the NHS in England
- 1. GENOMICS STRATEGY AND IMPLEMENTATIONIN THE NHS IN ENGLAND Professor Dame Sue Hill @CSOsue │ sue.l.hill@nhs.net Chief Scientific Officer for England and Senior Responsible Officer for Genomics in the NHS Central and South GMS Alliance conference November 22nd 2023
- 2. 2 Genome UK In 2020the government published Genome UK, a 10-year strategy to create the most advanced genomic healthcare system in the world. The strategy sets the direction for the UK genomics ecosystem, including the four devolved healthcare systems and other system partners, including Genomics England, National Congenital Anomaly and Rare Disease Registration Service, UK biobank, NIHR BioResource, Our Future Health and others. Diagnosis and personalised medicine Incorporating the latest genomic advances into routine healthcare to improve the diagnosis, stratification and treatment of illness Prevention Enabling predictive and preventative care to improve public health and wellness Research Supporting fundamental and translational research and ensuring a seamless interface between research and healthcare delivery Enabled by: • Engagement and dialogue with the public, patients and our healthcare workforce • Workforce development • Supporting industrial growth in the UK • Maintaining trust • Delivering nationally coordinated approaches to data and analytics
- 3. 3 NHS Genomics Strategy– published in 2022 UK Life Sciences Vision sets 10- year strategy for sector to solve some of the biggest healthcare problems of our generation including in cancer. Genome UK; the future of healthcare sets out a 10 year vision how we will achieve progress in genomic medicine across Diagnosis & Personalised medicine, Prevention and Research NHS Long Term Plan genomics commitments aligned to other policies for example cancer, cardiovascular, diabetes. Key themes include: 1. Embedding genomics across the NHS, through a world leading innovative service model from primary and community care through to specialist and tertiary care 2. Delivering equitable genomic testing for improved outcomes in cancer, rare, inherited and common diseases and enabling precision medicine and reducing adverse drug reactions 3. Enabling genomics to be at the forefront of the data and digital revolution, ensuring genomic data can be interpreted and informed by other diagnostic and clinical data; and 4. Evolving the service driven by cutting-edge science, research and innovation to ensure that patients can benefit from rapid implementation of advances Building on Genome UK and other government strategies, in 2022 NHS England published the NHS Genomics Strategy which outlines our vision for the power of genomics in predicting, preventing and diagnosing disease, and targeting treatment to be accessible to all as part of routine care in the NHS. The strategy sets out a 5 year action plan
- 4. 4 “Having a nationalhealth service allows for the uptake of genomics rapidly and at scale. The UK’s progress in implementing genomics also stems from the efforts of individuals who have championed genomics, whether at the grass roots level, in political or governmental and healthcare system leadership, or leaders of the medical community” This report identified the main challenges for embedding genomics: • the costs, availability, accessibility, and coverage of genomic testing; • the genomic literacy of specialists, primary care providers, and the public; • the need for clinical decision support tools; • availability of genetic counsellors as well as medical and laboratory geneticists; • clinical usefulness and actionability of findings; • the quality, diversity, and broad applicability of reference data sets; • computing infrastructure capabilities needed to analyse, store, share, and reanalyse vast amounts of genome sequencing data from within and across health care systems; • lack of professional guidelines The NHS is world-leading in implementing genomics
- 5. 5 The benefits ofembedding genomics
- 6. 6 The NHS GenomicMedicine Service launched in 2018 offers access to comprehensive genomic testing for all patients and the public in the NHS in England. This is made possible by our novel approaches to genomic medicine. NHS Genomic Medicine Service (GMS) with national oversight, contracting, resourcing, standard setting, management data & performance regimen 7 Genomics Laboratory Hubs (GLHs) 7 Genomic Medicine Service Alliances (GMSAs) 17 Clinical Genomics Services NHS Genomics Education Programme and other clinical services Our service model approach A multi-regional approach Embedding and equity is dependent upon the sharing of expertise across the country, and some services are being provided nationally. We also realise the benefits of both UK and international collaborations. A multi-professional approach Embedding requires involvement from all staff groups across the NHS. We are working with numerous professional groups, and have pursued cross-professional involvement in MDTs. A multi-specialty approach GMSAs have been – and will continue to be - key to embedding, maintaining a broad range of specialties and supported at all levels by clinical genomics. Serving all patients and the public A patient and public approach Involvement throughout the GMS governance structures to ensure services are co-created and co-designed and ongoing delivery is viewed through their lens Delivering a comprehensive offer Cellular Pathology Genomic Centres (CPGCs) Genomics England (WGS service and NGRL)
- 7. 7 NHS GMS geographies Requiressystems and partners working together to deliver a national Genomic Medicine Service for all patients and the public in the NHS in England.
- 8. 8 National Genomic TestDirectory – a national offer We drive equitable access through a single mandated National Genomic Test Directory focused on: (1) Rare and inherited disease; (2) Cancer ; (3) Pharmacogenomics These support a standardised offer of funded testing across England and a new pricing model Covers a full repertoire of testing through a multi-modal approach (single gene, panel tests, WES, WGS) Fast track application process which can respond to new developments, for example to reflect licensing decisions including for Olaparib and NTRK inhibitors. Cements WGS as central to service delivery Approximately 3,200 rare diseases and over 200 cancer clinical indications Updated annually through the Test Evaluation Working Groups. Through the Test Evaluation process to date, recent publication included tests such as whole genome sequencing for Sudden Unexplained Death in Childhood.
- 9. 9 NHS Genomic MedicineService: NGS from sample to result NHS Test Directory 1 Variants CNVs SVs 3 2 4 7 NHS Genomic Laboratory Hubs Variant calling Genomic Tumour Advisory Board
- 10. 10 1. Co-creating services,infrastructure and an operating model with patients and the public. 2. Developing a sustainable infrastructure across testing, clinical services and research and innovation. 3. Building greater clinical and professional leadership and developing the capacity and capability of the workforce. 4. Developing national and international collaborations and partnerships. Priorities Embedding genomics in the NHS, through a world leading, innovative service model 1 NHS Genomics Strategy National and global collaboration – France, Japan, Thailand, Singapore, Taiwan, India and Sweden Integrated governance and networks Key areas of progress Genomic training academies, NHS workforce strategy published, STP funding increased, international workforce summit Establishing Cellular Pathology Genomic Centres
- 11. 11 Education and training:supporting clinicians Creating national networks and a systematic approach to workforce development of the role of pharmacists in genomics and driving personalised medicine. Pharmacy programme Medical Programme Working with the Academy of Medical Royal Colleges to support the systematic roll out of genomic medicine within clinical pathways and to ensure clinicians have access to the right education and information at the right point Nurse & Midwifery led Genomics Collaborative Working with Chief Nurses across England to systematically and sustainably embed genomics into nursing and midwifery roles and responsibilities
- 12. 12 • Workforce agnostic,competency based • Bite sized integration of genomic medicine • Sharing of best practice: ‘do once and share’ • Avoids duplication; • Underpinned by robust evaluation. Integrating genomics into patient pathways: The Clinical Pathway Initiative (CPI)
- 13. 13 Delivering equitable genomic testing for improved prevention, diagnosis,and precision medicine 1. Systematically introducing new clinical indications for genomic testing and embedding comprehensive genomic testing within end to end clinical pathways. 2. Driving the use of precision treatments and optimising the use of medicines through genomics. 3. Enabling the rapid evaluation and adoption of affordable, efficient, and innovative genomic technologies Priorities 2 Evolving the genomic testing strategy Aligning clinical trial targets with standard of care and working to nationally agreed cancer turnaround times Key areas Working with NICE to establish a genomic med tech pathway
- 14. 14 Alignment with treatmentintervention • Variation to drug response affected by multiple factors, including genetic and epigenetic variation1,2 - responses to drugs 25-80% • NHS - £17.1 billion in drug spend per annum3 • An additional £2.2 billion estimated due to Adverse Drug Reactions (ADRs)4 - contribute to 8.5 - 5.6% of hospital admissions • Genomic and precision medicine, and pharmacogenomics have the potential to individually characterise causes and optimise treatment for patients5 • Pre-emptive pharmacogenomic testing and subsequent evidence-based pharmacogenomic interventions recently shown to reduce incidence of ADRs.6 • Personalised medicines accounted for more than 25% of FDA approvals for each of the last eight years, mostly for cancer or rare disease 1.Grant M, NHS England 2016, 2. Spear, Trends Mol Med 2001, 3.NHSBSA,2021 4.Osanlou BMJ Open, 2022, 5. Pirmohamed, Nat Rev Genetics 2023, 6. Swen JJ, Lancet, 2023
- 15. 15 NHS Genomics MedicineService Transition driven by: ▪ Cost (for depth) ▪ Performance ▪ Turnaround times ▪ Value/benefit of test ▪ Number of tests vs tissue volume Future direction: single WGS to capture clinical and research requirements Current Practice SNVs CNVs Fusions TMB HRD MSI FISH Cyto- genetics IHC for Diagnosis Pharmaco- genomics DPYD Deficiency Inherited cancers (germline) National Test Directory https://www.england.nhs.uk/publication/nati onal-genomic-test-directories/ NGS creates a ‘One Stop Shop’ for diagnosis
- 16. 16 | Non-small celllung cancer as an example of end to end pathways that are needed to be established There are 8 genomic targets in NSCLC for which there are licensed targeted drugs. All 8 have a NICE- approved treatment option. • Currently 2100 patients/year treated: 1700 as initial treatment, 400 as subsequent therapy. • EGFR exon 19 and 21 mutations: osimertinib 1000 patients/year for initial therapy of advanced disease, 200/year as adjuvant therapy after resection • ALK alterations: 250/year initial therapy, split between alectinib and brigatinib • ROS1 alterations: entrectinib 50/year initial therapy • MET exon 14: tepotinib 70/year initial therapy and 50/year subsequent treatment • KRAS G12C: sotorasib 300/year subsequent treatment • BRAF: dabrafenib plus trametinib 70/year initial therapy • EGFR exon 12: mobocertinib 70/year • RET fusion: 25/year for subsequent treatment but now initial therapy access this month.
- 17. 17 Impact of clinicalpractice gaps on the delivery of precision oncology for advanced NSCLC 64% of potentially eligible patients with advanced NSCLC are not benefiting from precision oncology therapies. Addressing practice gaps and building sustainable care infrastructure are critical to deliver on the promise of precision medicine. Source: Sadik et al. JCO 2022
- 18. 18 Driving the useof personalised treatments - optimising the use of medicines through genomics Use cutting-edge technology to deliver tailor-made genetic material into a patient’s cells to treat disease and inclusive of newer rare disease treatments eg ASOs Gene therapies & ATMPs Based on an increased understanding of the genomic basis for disease and diagnosis particularly in cancer and increasingly in rare disease New targeted treatments Guide treatment decisions and dosing using genomic data to predict adverse drug reactions Pharmacogenomics New indications for existing medicines Repurposing Drug resistance and pathogen resistance Predicting From novel therapeutics To optimising existing medicines
- 19. 19 Thousands of cancerpatients are benefitting from the introduction of DPYD testing which can prevent adverse drug reactions and NTRK gene fusion testing to support new histology independent cancer treatments The rollout of Non-Invasive Pre-natal Diagnosis for Retinoblastoma is one of more than number of new tests and amendments to the National Genomic Test Directory The GRAIL partnership is looking at early detection of cancer and is being piloted in 165,000 people from the general population will report in 2025. A ctDNA pilot in NSCLC with Guardant (and Roche) is showing average overall detection rate for actionable mutations with targeted therapies was 21.5% and leading to technology transfers Oliver was born with a 6cm lump on his leg and initial investigations suggested infantile fibrosarcoma. He was referred for WGS and it was found that the mass was in fact a myofibroma, a benign tumour so no treatment was needed. In Paediatric cancers In cystic renal disease WGS led to clinical action in 48% of those tested and 71% of those with a diagnostic variant inclusive of use of Tolvaptan or decision to transplant or informing surveillance frequency Cancer: Blood test for 50 types to be trialled by NHS NHS to pilot blood test that could detect over 50 different cancer types Gene test spares baby unnecessary chemotherapy Transformative genomic medicine in practice
- 20. 20 1. Developing aninteroperable informatic and data infrastructure that enables the NHS to use and share genomic data appropriately to improve patient care. 2. Putting the NHS at the forefront of using genomic data alongside other health data to drive health improvements for individuals and populations. 3. Enabling the NHS to use cutting-edge analytical tools and up to date variant databases to maximise diagnosis, access to precision medicine and efficiency. Priorities Implementation Plan – Priorities Identified Genomic Data and Digital Steering Group established Genomic Data and Digital framework in development Interoperability (Phase 1) : Master Data Set validation complete Unified Genomic Record Digitised Test Directory Better coordination and interoperability Enabling genomics to be at the forefront of the data and digital revolution 3 Key areas of progress
- 21. 21 Data generation inthe NHS Genomics Medicine Service “With personal technology, doctors can see a full, continuously updated picture of each patient and treat each individually” Topol. 2014. Cell 1. Genomic data – generated from genomic testing, including phenotyping and staging data to enable interpretation. The value of this genomic data can only be maximised if linked with other diagnostic and clinical data sources across the life course often at a national level and in standardised formats. 2. Clinical data – where additional patient data, for example clinical symptoms, and longitudinal health data are used to inform genomic analysis and ongoing research insights. 3. Management data – for operational improvement and evaluation – national collection of the genomic testing activity, variation in access, turnaround times and linked with outcomes and treatment data.
- 22.
- 23. 23 1. Enabling patientsto make informed choices on the use of their data for research and innovation. 2. Enriching existing and developing new NHS GMS relationships to support innovation and the generation of evidence for adoption and improvements in health and care. 3. Ensuring ongoing alignment with clinical trials and national life sciences projects and supporting the growth of life sciences in the UK Priorities Evolve the NHS GMS Research Collaborative Planning with Genomics England to initiate the Generation Study Better coordination and understanding of genomics research to ensure developments fed into the NHS for patient benefit Research to be delivered at scale and speed Increasing volume of high- quality genomic research in the NHS with reliable genomic insights that are easy to request and interpret Researchers through data, infrastructure and insights to collaborate and accelerate fundamental and translational research Evolving the service through cutting-edge science, research and innovation 4 NHS Genomic Networks of Excellence agreed and to be established in 2023/24 Key areas
- 24. 24 The NHS CancerVaccines Launch Pad The NHS Cancer Vaccines Launch Pad (CVLP) is designed to act as a bridge to enable NHS cancer patients to get the earliest possible access to personalised cancer vaccine trials and other immunotherapies, by providing a defined and expanded standard of care pathway for tumour molecular analysis and sequencing incorporating elements of the NHS Genomic Medicine Service. Tissue Sampling Pathway Genomics Pathway Data infrastructure
- 25. 25 Central and SouthGLH Phase One Sites • CPGC • Thames Valley/Oxford • Wessex/ Southampton • North West Midlands/ BCPS • CVLP • Oxford; sample route to Oxford • Southampton: sample route to Southampton North West Midlands CPGC lead site: BCPS CVLP samples: site not identified Thames Valley CPGC lead site: Oxford CVLP samples: Oxford Wessex CPGC lead site: Southampton CVLP samples: Southampton
- 26. 26 Linking with GenomicsEngland and the NGRL for WGS Diagnostic Discovery Accelerating genomic research Evolving genomic healthcare DISCOVERY TRANSLATION ADOPTION DIFFUSION Through the National Genomic Research Library (NGRL) populated with 100,000 Genome Project and consented deidentified NHS GMS WGS data. Establish putative pathogenicity of VUS Researchers granted access to the deidentified NGRL database to review genomic and clinical data Ongoing variant interpretation from diagnostic discovery and return of WGS results to GLHs from the GMS service informs genes on panel app and the semi automated pipeline and evidence informs the National Genomic Test Directory and clinical guidelines Diagnostic discovery Deidentified data Reporting of results Over 1,500 putative diagnostic discoveries have been returned to the NHS Results from diagnostic discovery are reidentified by GEL reviewed and further validated by GLHs and feedback to clinicians
- 27. 27 Establishing NHS GenomicNetworks of Excellence During 2023/24 NHS England will, as part of the evolving NHS GMS Alliance infrastructure, establish ‘NHS Genomic Networks of Excellence’ NHS Genomic Networks of Excellence will be partnerships between the NHS, academia, the third sector and industry to generate evidence and models of adoption for new technology and testing and, clinical and laboratory practice in defined topic areas of strategic importance. DISCOVERY TRANSLATION ADOPTION DIFFUSION NHS England has confirmed funding for: ► Prenatal Genomic Medicine Network of Excellence ► Circulating Tumour Biomarker testing for rapid diagnostics and monitoring for Cancer of Unknown Primary, advanced metastatic Breast Cancer, Paediatric Cancer, circulating miRNA test for Germ Cell Tumours and CSF testing for primary CNS lymphoma. ► Haemato-Oncology NHS Genomic Network of Excellence including rapid WGS ► NHS Rare and Inherited Disease Genomic Network of Excellence ► Severe Presentation of Infectious Disease Genomic Network of Excellence using long read sequencing in a partnership with Oxford Nanopore ► Improving the identification and outcomes for individuals with inherited and acquired cardiovascular disease NHS Genomic Network of Excellence ► Pharmacogenomics and Medicines Optimisation NHS Genomic Network of Excellence focusing on primary care, mental health, as well as specific drug/gene pairs ► Genomics Artificial Intelligence (AI) NHS Genomic Network of Excellence
- 28. 28 Supporting life sciencesprojects in pathways to adoption Diverse Data Making data and analytics more powerful to support our diverse population linking for example with NHS sickle cell blood group genotyping programme Long-read Sequencing To support rapid, precision NHS diagnostics and treatment planning closer to the patient using Oxford Nanopore technology as well as a rare disease project comparing long read with short read sequencing and mulitomic profiling Our Future Health The UK’s largest ever health research programme through the discovery and testing of more effective approaches to prevention, earlier detection and treatment of diseases. Aligning with research infrastructure & investment Working with the NIHR Biomedical Research Centres and MRC Research Nodes to advance genomics research Supporting research studies Supporting cutting edge research studies, for example the Population Architecture using Genomics and Epidemiology (PAGE) study and the Deciphering Development Disorders (DDD) Study, and many others Newborns Genome Programme Delivering the NHS-embedded Generation Study, to explore the benefits, challenges, and practicalities of sequencing and analysing newborns' genomes
- 29. 29 The ecosystem ofgenomic medicine is constantly developing. We value - and credit our major successes – to the partnerships and learning loops that we have established in the UK and internationally. Sharing data, tools, experience, and knowledge to create a global “learning health system” is essential if we are to effectively accelerate and sustain the integration of genomics into healthcare Areas for engagement include: • Exchanging information, sharing data and best practice including adoption and embedding of genomic medicine at scale • Establishing evidence synthesis against agreed policy domains • Agreeing common standards and outcome metrics • Enhancing interpretation of complex information and establishing global resources • Communication and engagement Maximum benefit Academia International NHS & other health systems Charities & professional bodies Patients Industry Establishing successful partnerships
- 30. 30 Making Genomics mainstreamin medicine: 2020 and beyond BIG QUESTION: Can we deploy genomics broadly and equitably in medicine? Green et al. (2020)
- 31. 31 Call to action Identifyareas of unmet need or inequalities that require concerted action Work together to coordinate and embed genomics across NHS pathways and clinical specialties to inform earlier decision making in conjunction with the NHS GMS infrastructure Utilise the available and funded genomic testing for all defined conditions in all NHS Trusts and across the care continuum Support the tissue pathway developments and Cellular Pathology Genomic Centres to enable the comprehensive genomic analysis of cancers by the NHS GLHs for all patients Develop and support the multi-professional workforce to be leaders in genomics and to be upskilled to use and interpret genomic information and to support patients and their families Enable the monitoring of access to precision treatments and interventions based on genomic data Support continued research and innovation projects and initiatives in the UK Life Sciences sector and enable the ongoing population of a national genomic research library