The Scottish Genomes Partnership

Lead Research Organisation: University of Edinburgh

Abstract

The genome is the complete set of genetic material in each of the cells of our body, inherited from our parents. Sometimes, changes (mutations) happen that cause disease. If someone has a disease, it’s now possible and affordable to read their genome to see if it might be caused by a mutation. If it has, scientists can use that information to understand the disease better, and perhaps one day treat or cure it. The UK's Department of Health (DH) set up its own company called Genomics England (GeL) to sequence the genomes of consenting families or individuals who suffer from rare genetic diseases and cancers. GeL has £100m from DH England to sequence 100,000 genomes. The MRC wants to work with the Devolved Governments of Northern Ireland, Scotland and Wales to help to develop in genome sequencing too, and to contribute to the 100,000 genomes project through GeL. We hope to help build a UK-wide partnership that can deliver better and faster results for patients.
This award is the MRC’s investment in the Scottish Genomes Partnership (SGP). It partners funding of £4,000,000 from the Scottish Government, and up to £3,500,000 from Scottish Enterprise. Together, funds will be used to (1) support SGP's sequencing of 1000 genomes of people with rare diseases (and often also their families) and (2) to address the challenge of how to provide researchers with appropriate access to, and use of, complex data stored across more than one secure site.

Technical Summary

As part of a strategy to deliver genomic medicine in the NHS, Genomics England (GeL) was allocated £100m by DH England to sequence 100,000 genomes. The MRC wished to partner the Devolved Governments of Northern Ireland, Scotland and Wales to help to develop their capabilities and support their engagement with this initiative through GeL, to help to establish a UK-wide partnership that builds and brings together larger assets of genomic data from across the UK, with the capability to link together and enhance genomic, phenotypic and health record assets.

This award represents the MRC’s investment in the Scottish Genomes Partnership and complements partnership funding of £4,000,000 from the Scottish Government, and up to £3,500,000 from Scottish Enterprise, which will be awarded separately. Funds will be used to (1) support SGP's sequencing of genomes of individuals with rare diseases (1000 genomes, ca 330 trios) and (2) to support the development of federated analysis solutions for distributed genomic data, including through joint working with GeL.

Publications

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Cooke SL (2017) The Driver Mutational Landscape of Ovarian Squamous Cell Carcinomas Arising in Mature Cystic Teratoma. in Clinical cancer research : an official journal of the American Association for Cancer Research

 
Description Edinburgh visit of Illumina CEO, CFO and CTO to Edinburgh Genomics facilities and SGP
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Informing the Future of Medical Genomics in Scotland, Precision Medicine Summit
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Contributions to BEIS report on Precision Medicine and consideration by Scottish Government.
 
Description Member, European Research Council Advanced Grant Panel LS2
Geographic Reach Europe 
Policy Influence Type Membership of a guideline committee
Impact Award of European Research Council Advanced grants.
 
Description Priorities for Translational Research and Innovation in Scotland, Scottish Policy Conferences, Cancer Care
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Raising the profile of genomic research to the attention of the Scottish Government.
 
Description Scottish Clinical Genetics Research Day
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Enhancement of Scottish clinical genetics research and knowledge and understanding of genomic tools available.
 
Description Scottish Genomes Partnership - Scottish Science Advisory Council
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact Working with the Scottish Science Advisory Council, raising the profile of Genomic Medicine and the potential for its future use to the Scottish Government via the publication of the report "Informing the Future of Genomic in Scotland"
 
Description Scottish Parliament Inquiry into Genomics in Healthcare for Scotland - Scottish Scientific Advisory Council
Geographic Reach National 
Policy Influence Type Participation in a national consultation
Impact New funding proposal under consideration. Scottish Genomes Catalyst Fund, £3.5M, under auspices of Scottish Enterprise, now under review.
 
Description The Ethics of Genomic medicine, Royal Medical Society
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Raising the profile of ethical issues surrounding genomic research amongst medical communities.
 
Description Visit of Cabinet Secretary for Health and Sport to Edinburgh Genomics
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Raising the context of Scottish genomics to the attention of the Scottish Government.
 
Description Visit of Scottish Cabinet Secretary for Health and Sport to Scottish Genomes Partnership and subsequent policy dialogue
Geographic Reach National 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
Impact Proposal now under consideration by Scottish Government for future funding of genomics in healthcare.
 
Description Written and oral evidence to House of Commons Science and Technology Committee inquiry into Genomics and Genome Editing
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
Impact Gave UK-wide context to genomic medicine, particularly the participation of the devolved administrations and the interactions between Scottish and English national genome projects. Increased awareness of the SGP award and its impact in the Westminster and Scottish Parliaments.
URL https://www.parliament.uk/business/committees/committees-a-z/commons-select/science-and-technology-c...
 
Description Early Detection Committee - Project Award
Amount £483,949 (GBP)
Funding ID C22524/A26254 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2018 
End 11/2021
 
Description Whole Genome Sequencing for Health and Wealth Initiative
Amount £2,000,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 02/2016 
End 01/2018
 
Title Scottish genetic variant archive 
Description Where ethically authorised, all variants sequenced in the Scottish Genomes Partnership are being collated into a Scottish variant archive for wide use by academics, healthcare and other bona fide users. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact Database under construction and will be presented to (a) the SGP Scientific Advisory Board in April 2018 and (b) to a wider academic and professional audience by Q1 2019. 
 
Description AstraZeneca Annual Genomics Partners Workshop 
Organisation AstraZeneca
Country United Kingdom 
Sector Private 
PI Contribution I made proposals for collaborative research with AstraZeneca.
Collaborator Contribution I sit on the AstraZeneca genomics advisory board.
Impact No impact yet
Start Year 2018
 
Description Cell-Free DNA Opportunities for Cancer Diagnostics 
Organisation Cancer Research UK
Department Edinburgh Cancer Research UK Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution We are developing strategies for analysis of cfDNA for early detection and diagnosis of cancer,
Collaborator Contribution We carry out in silico and wet lab investigation of cfDNA across several cancer types, in collaboration with oncologists and cancer surgeons in the Scottish NHS.
Impact No impact yet.
Start Year 2018
 
Description Genetic Studies of Motor Neurone Disease - SGP SAB 
Organisation Scottish Genome Partnership
Country United Kingdom 
Sector Learned Society 
PI Contribution We sequenced the genomes of 380 patients with motor neurone disease.
Collaborator Contribution We analysed the genome sequences and compared to controls. The data are part of an emerging collaboration with the New York Genome Center to identify disease genes for motor neurone disease.
Impact No impact yet
Start Year 2016
 
Description Genomics England partnership for sequencing patients in the Scottish NHS 
Organisation Genomics England
Country United Kingdom 
Sector Public 
PI Contribution Collaboration agreement signed, secure data transfer in place, genome sequence data being analysed collaboratively.
Collaborator Contribution Recruitment and sequencing of 1000 genomes of patients and their families in the Scottish NHS
Impact Written and oral evidence to House of Commons S&T Committee Inquiry in Genomics and Genome Editing
Start Year 2016
 
Description Liquid Biopsy and Early Detection, CRUK Brain Cancer Centre of Excellence Workshop 
Organisation Cancer Research UK
Department Edinburgh Cancer Research UK Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution We are developing strategies for analysis of cfDNA for early detection and diagnosis of cancer.
Collaborator Contribution We carry out in silico and wet lab investigation of cfDNA across several cancer types, in collaboration with oncologists and cancer surgeons in the Scottish NHS.
Impact No impact yet
Start Year 2018
 
Company Name BIOCAPTIVA LIMITED 
Description BioCaptiva produce a medical device designed for extra-corporeal DNA capture from the blood by means of apheresis. Using the device cell-free DNA in the blood can be bound to a specifically designed polymer fixed to a matrix in an apheresis system. This allows for isolation of cell-free DNA in quantities unavailable via a traditional blood-draw, allowing for the detection of circulating-tumour DNA. 
Year Established 2018 
Impact No notable impacts to date.
 
Description Advanced Medicine: Introduction to Genomics, Advanced Medicine Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This was a lecture at the Royal College of Physicians Advanced Medicine symposium, attended by over 200 trainees policymakers and others.
Year(s) Of Engagement Activity 2018
 
Description Edinburgh Medical Debate - proposed motion 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact The subject matter of the debate was: "Edinburgh Medical Debate. Genome Screening: A Pandora's Box?". The motion for the debate was: "This house believes that the UK population should have whole genome screening." As proposer of the motion, we had pre-debate support for 36% of the audience, and post-debate support of 47%. A swing of 11% in favour of the motion!
Year(s) Of Engagement Activity 2017
URL https://media.ed.ac.uk/media/Edinburgh+Medical+Debate.+Genome+ScreeningA+A+Pandora%27s+BoxF/1_6nqurm...
 
Description Genomic Medicine: Yesterday, Today and Tomorrow 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This was a lecture at the joint meeting of Genomics England and Brisith Society for Genetic Medicine, attended by over 200 clinicians, trainees and others.
Year(s) Of Engagement Activity 2018
 
Description Invited presentation to Royal College of Physicians of Edinburgh: "Genomic Medicine in Scotland: Progress, Prospects and Promises" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation to RCPE Senior Fellows - to inform and influence.
Year(s) Of Engagement Activity 2017
 
Description New perspectives, new opportunities in life science and healthcare, BioDundee 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This was a lecture at the Biodundee healthcare research symposium, attended by over 100 trainees policymakers and others.
Year(s) Of Engagement Activity 2018
 
Description Opening presentation at Royal College of Physicians, Advanced Medicine Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited presentation on impact of advances in genomics on clinical practice.
Year(s) Of Engagement Activity 2018
URL https://www.rcplondon.ac.uk/events/advanced-medicine-2
 
Description Opening presentation, British Society for Genetic Medicine, Royal College of Physicians of London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited presentation on the Scottish Genomes Partnership and Scottish collaboration with Genomics England
Year(s) Of Engagement Activity 2017
URL http://www.bsgm.org.uk/bsgm-annual-meeting-2017/
 
Description Presentation at Scottish Parliament - Rare Disease Day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Prof Zosia Miedzybrodzska, Lead Clinical Geneticist on this award, and for Scotland, gave an invited presentation on the Scottish Genomes Partnership and genome sequencing therein. Over 150 people from patient organisations, the public, and members of the Scottish Parliament including the Minister for Mental Health and the Chair of the Cross-Party Group on Rare Diseases were present.
Year(s) Of Engagement Activity 2018
URL https://www.scottishgenomespartnership.org