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TRANSCRIPT
The 100,000 Genomes Project
Dr Cheryl Flanagan
Molecular Pathology Services Project Manager
Rare Disease Day 2017
28th February
Background
The first human genome sequence
• 100,000 Genomes at Millennium Prices - Cost $320
trillion
• 26th June 2000 - Cost $3.2 billion
Cost per genome
Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP) Available at: www.genome.gov/sequencingcostsdata. Accessed [10/10/16]
The 100,000 Genomes Project
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Background
Announced by the former Prime Minister in December 2012
An Olympic Legacy
Genomics England announced by Secretary of State for Health in speech during NHS 65th Anniversary Celebrations, July 2013
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Chief Medical Officer Recommendations
• 2013 - Professor Dame Sally Davies established a Strategic Priorities Working Group for the Project - chaired by Professor David Lomas (UCL)
• Recommended rare diseases, certain cancers, and infections.
• Areas where they believe the introduction of genomic technology will have the greatest benefit for patient health.
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Accessible at https://www.genomicsengland.co.uk/library-and-resources/
Rare disease
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Why make genetic diagnoses?
1. For the patient
• Understand why their condition happened
• More accurate knowledge of how it might develop in future
• Possible treatment avenues
• Contact with others with the same condition
2. For the family
• Predict whether family members will get the condition
• Offer screening/treatment to prevent it
• Reproductive decisions
3. For medical research
Aims:
• Source expert knowledge to establish a final diagnostic grade gene panel (green list) for each disorder that will be used in the classification of genetic variants to aid clinical interpretation of rare disease genomes
• Engage Scientific Community, encourage open debate, and begin to establish consensus on gene panels for rare diseases.
• Standardisation of terms and collection of gene-disease related information, accumulation of reviews over time, and updated releases
Rare disease programme
• Over 200 disorders so far
Data model: describes the clinical information to be collected for each disorder
Disorders nominated by the NHS and academia
Eligibility criteria: describe which patients to recruit
Gene panel: the genes to be analysed first for patients with that disorder
First families diagnosed from the Newcastle BioResource pilot
Leslie Hedley, 57
WGS revealed Mr Hedley’s kidney failure was caused by a particular genetic variant (INF2 mutation). His family is also being tested and their blood pressure can now be effectively controlled by drugs available on the NHS.
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Jessica Wright, aged 4Georgia Walburn-Green, aged 4
First children receive diagnoses (GOSH)
The 100,000 Genomes Project
Four main aims
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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
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Key Operational Features
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Genomics England - a company wholly owned by the Department of Health
Sequencing 100,000 genomes
Clinical service, major research project and NHS transformation
Focusing on cancer, rare disease (and infection - Public Health England)
Based on consent
Linking phenotypic and medical record data with genome data
13 NHS Genomic Medicine Centres England & NI
Data held in a secure and monitored environment with strictly regulated access for researchers including industry
Genomic medicine education programme lead by Health Education England is embedded in the NHS to upskill the workforce
Over 2000+ scientists and clinicians engaged through disease-based Genomics England Clinical Interpretation Partnership (GeCIPs)
Additional funding through MRC, the Wellcome Trust
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NHS England & NHS Genomic
Medicine Centres
GeCIP Domains
IndustryPartnerships
Genomics England
Illumina
The Principal Partners
How it works
Establishment Phase• Illumina - NHS Genomic Medicine Sequencing Centre in
Hinxton (village in South Cambridge)
• UK Data Infrastructure for Genomic Medicine (with MRC)
• NIHR National Biosample Centre - £24 million state-of-the-art facility to store the samples
• NHS Genomic Medicine Centres (GMC’s) – over 85 Health Trusts, 1,500 NHS Staff (doctors, nurses, pathologists, laboratory staff, genetic counsellors)
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Data CentreNHS Genomic Medicine Sequencing
CentreNIHR Biosample centre
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NHS Genomic Medicine Centres
Responsible for identifying and recruiting participants and for clinical care following results
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• 13 Genomic Medicine Centres covering England
• Devolved Nations Genomic Medicine Centres
• October 2015 Health Minister in the NI, announced £3.3m investment NI Genomic Medicine Centre (NIGMC)
• The creation of the NIGMC is one of the first actions in the NI Rare Diseases Implementation Plan
• Current partners - DoH; HSCB; PHA; PathNet; QUB; UU; PPI; GEL; MRC
• Future partners include DfE; NI Industry; Invest NI; other funders
• Discussion between NI & RoIGovernments
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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
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Additional findings offered in the 100,000 Genomes Project
OPTIONAL!
Requirements:• Reliably detected by genome
sequencing• Curated list of high confidence, high
penetrance variants• Treatable or preventable condition
Other conditions may be added if clinically appropriate and technically feasible
Genomics England Clinical Interpretation Partnership (GeCIP)
• Launched at the Wellcome Trust in June 2014
• Partnership between over 2,000 researchers from academia and the NHS, trainees, plus international collaborators.
• Designed to accelerate academic/industry partnership and development of diagnostics and therapies
• Over 35 topics (domains) of research and most domains cover a single disease or group of diseases and some are wider e.g. epigenomics, health economics and technology.
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Working with the research community
• All data generated contributes to the Genomics England Dataset
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GENE ConsortiumWorking with industry
• 12 companies = the Genomics Expert Network for Enterprises (GENE) Consortium to oversee a year-long Industry Trial
• Aims to identify most effective and secure way to accelerate development of new diagnostics and treatments for patients
• Range from big pharma to small biotech
• Working in a pre-competitive environment
• AbbVie, Alexion, AstraZeneca, Berg, Biogen, Dimension Therapeutics, GSK, Helomics, Roche, Takeda, NGM Biopharmaceuticals, UCB
Health Education England
• 11 University providers of MSc in Genomic Medicine • Aimed at NHS healthcare professionals working in England
• Full/part time study
• Fully funded places available through HEE
• Individual (CPPD) modules available for range of professional backgrounds and groups (e.g. medicine, nursing, healthcare scientists and technologists).
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Genomics Education Programme
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• Online training courses and resources • The fundamentals of genomics• Bioinformatics • The consent process
National Participant Panel
• Includes current participants, quarterly meetings
• Members sit on key committees including the Data Access Review Committee, GeCIP Board, Ethics Advisory Committee
• Produce and input in materials e.g. flyers, leaflets, animations
https://www.genomicsengland.co.uk/about-genomics-england/how-we-work/patient-and-public-involvement/
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Project’s progress so far
• Sequenced over 26,000 whole genomes, with over 19,000 in the datacentre.
• Protocols, standards and data infrastructure that are being developed will ensure frontline clinicians can make the most of the knowledge that genomics provides, for patients now and in the future.
• An automated reporting pipeline has been built, and results are now being returned to clinical teams across the NHS to use in patient care.
http://www.genomicsengland.co.uk/updates/
Building the future of genomic medicine• 100,000 WGS on NHS patients and pathogens
• Concentrating the UK Genomics Knowledgebase in one location
• The NHS, academics and industry partnerships at the outset to drive Genomic Medicine into the NHS and create wealth
• Building the human capacity and capability
• Key international partnerships to add value
• Leave a legacy of NGS Centres, sample pipeline and biorepository, large-scale data store that makes this usable by the NHS
• New diagnostics and therapies and opportunities for patients
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