Genomics and personalised medicine

Transcription

1 Genomics and personalised medicine Dr Tom Fowler, Deputy Chief Scientist & Director of Public Health WHO Symposium on the Future of Digital Health Systems in the European Region February 2019

2 About me Tom Deputy Chief Scientist & Director of Public Health, 100,000 Genomes Project 100,000 Genomes Project Sequencing 100,000 genomes from around 85,000 people. Participants are NHS patients with a rare disease, plus their families, and patients with cancer. NHS Genomic Medicine Service Supporting the implementation of a national Genomic Medicine Service in England. 1. To bring benefit to NHS patients 2. To create an ethical and transparent programme based on consent 3. To enable new scientific discovery and medical insights 4. To kickstart the development of a UK genomics industry 2

3 Reaching 100,000 On 5 December 2018, the Health and Social Care Secretary announced that Genomics England reached the major milestone of 100,000 whole genomes sequenced From here, we are still working hard to turn around returning results to the Genomic Medicine Centres We are also working in partnership with NHS England to deliver 1 million genomes, as part of the Health and Social Care Secretary s ambition to sequence 5 million genomes As of February 2019, we have sequenced over 104,000 whole genomes from patients and their families 3

4 From 100,000 to 5 million 500,000 whole genomes through the Genomic Medicine Service Plus other genomic tests 500,000 whole genomes through upgrade of UK Biobank sequencing Whole genome sequencing of strategic cohorts (unmet needs and long term value to the healthcare system) Research cohort sequencing (whole genome and other genomic tests) funded by current and future funding Exploratory programme for self-paying volunteers who wish to be early adopters of genomic analysis 4

5 How the 100,000 Genomes Project works 13 NHS Genomic Medicine Centres covering England, over 90 hospitals Responsible for identifying and recruiting participants and for clinical care following results Northern Ireland, Scotland and Wales have now joined Discovery Forum Industry Users 5

6 Definition of public health The science and art of promoting and protecting health and well-being, preventing ill-health and prolonging life through the organised efforts of society. The Acheson Report, London,

7 The four P s of personalised medicine 1. Prediction and prevention of disease 2. More precise diagnosis 3. Targeted and personalised interventions 4. A more participatory role for patients 7

8 Improving outcomes through personalisation Improves outcomes Targeted therapy Identification of effective personalised treatments Accelerated diagnosis based on underlying cause and incidental findings rather than just grouped symptoms Early disease detection 2-8 yrs before onset & symptoms become obvious with low cost stratification Targeted disease prevention Identification of predisposition markers or underlying processes can predict future disease Delivering the 4 Ps of Personalised Medicine Prediction (& prevention) of disease, More Precise diagnoses, Personalised and targeted interventions More Participatory role for patients 8

9 Shaping healthcare through a wealth of new information Technology, Innovation & Knowledge Base Clinical Change Model DNA Genomics Transcriptomics Informatics and digital health Phenotypic characterisation & diagnostics Patient Self-reporting Proteomics Metabolomics Personalised Therapeutics Policy & System Alignment Infrastructure 9

10 Scalable rare disease diagnostics DNA Patient/ family Phenotypes & Pedigree Clinical assessment Validation Outcomes GeCIP(s) Gene Panels Report QC Reporting tool Genome sequence Annotated VCFs Gene Panel Variant filtering Tiered variants Review Annotation Companies

11 The vision: A move from illness to health ILLNESS Delayed diagnosis Late stage disease Multiple conditions Restricted treatment & management options Poorer outcomes & patient experience HEALTH Using science and technology to improve outcomes and health through Prognosis Earlier disease stages offering more treatment options Influencing lifestyle factors Stratified medicine This will deliver the 4 Ps of Prediction (& prevention) of disease 11

12 The ethical frontline of scientific advance Many new technologies are bringing with them ethical challenges - such as the use & handling of data, or if they have predictive ability but issues can occur if science is felt to move too fast. or too slowly How far should the science go? Are the public ready? 12

13 Patient involvement - the National Participant Panel Role of the Panel is to ensure the interests of participants are always at the centre of the 100,000 Genomes Project. They do this by: Making sure experiences of participants are at the heart of the project Responding to feedback Overseeing who should have access to participant data Access Review Committee GeCIP Board Ethics Advisory Committee Discovery Forum Participants 13

14 Genomics England Clinical Interpretation Partnership (GeCIP) A research consortium with over 3,200 researchers from academia and the NHS, trainees, plus international collaborators (over 2,100 currently eligible for data access) Currently 37 out of 42 domains have been approved We have now received suggestions of diagnoses for 41 families from the Research Environment Includes GeCIP and Discovery Forum users Includes both: new, clear-cut diagnoses new discoveries/research collaborations 14

15 Genomics England Stakeholders The Discovery Forum Business value Discovery Forum Exploring the business value of genomic medicine data. Industry Stakeholders Connecting industry stakeholders to the Genomics England community. Research Environment Genomic dataset Health service Stakeholders Academic Stakeholders Providing a gateway to our Research Environment and dataset. Leading to discovery and development of precision methods, diagnostics, and therapeutics. Over 100 Discovery Forum members (9 full members). 15

16 Data in our Research Environment Genomes 80,883 genomes 19,305 Cancer 61,578 Rare Disease Primary clinical data 85,070 participants 17,062 Cancer 68,008 Rare Disease Secondary data* Hospital Episode Statistics (HES) Diagnostic Imaging Dataset (DID) Patient Reported Outcome Measures (PROMs) Mental Health Services Data Set (MHSDS) Office for National Statistics (ONS) mortality data and cancer flagging Clinically interpreted data & QC 16,659 families with Tier 1, 2 and 3 variants from interpretation pipeline 2,469 families with GMC exit questionnaires 31,686 tiered and quality checked rare disease genomes; 12,537 quality checked cancer genomes Quick view tables Key information from different tables, merged and filterable Merged with QC data Allow cohort-building and project feasibility assessment * Secondary data is available up to January 2018, and will be updated as soon as possible 16

17 What are we telling participants? Information about a patient s main condition Information about additional serious and actionable conditions (optional) Carrier status for non affected parents of children with rare disease (optional) Image courtesy of Health Education England 17

18 Building the future NHS Genomic Medicine Service As of 2019 the NHS now: Has a national Genomic Medicine Service providing consistent & equitable care for 55 million population Is operating to common national standards, specifications & protocols Has standardised genomic consent for NHS care and Research Is delivering an approved national testing directory covering use of single gene to WGS Is building a single UK Genomic Knowledgebase Has a national NHS database with all tests that will enable care, effectiveness, and outcomes Has de-identified data for academic & industry research 18

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20 Credits Chief Scientific Office for NHS England, Prof Sue Hill PHG Foundation Academy of Medical Sciences 20

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