The Scottish Genomes Partnership

Lead Research Organisation: University of Edinburgh
Department Name: UNLISTED

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

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De Boer E (2022) Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein. in Genetics in medicine : official journal of the American College of Medical Genetics

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Dulias K (2022) Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney. in Proceedings of the National Academy of Sciences of the United States of America

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Ewing A (2021) Structural Variants at the BRCA1/2 Loci are a Common Source of Homologous Repair Deficiency in High-grade Serous Ovarian Carcinoma. 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 National Diagnostics Advisory Group
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact Sponsorship and engagement with the pharmaceutical company Bristol Myers Squibb is leading to economic development in Scotland and across the UK.
 
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 Genomics Leadership Group
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
Impact Research and practice implications for whole-genome sequencing, liquid biopsy and COVID-19 testing.
 
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 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 Molecular Pathology Nodes Call Feb 2015
Amount £1,990,267 (GBP)
Funding ID MR/N005902/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 08/2015 
End 08/2018
 
Description Scottish Genomes Partnership Agreement Extension
Amount £1,044,181 (GBP)
Funding ID SGP/2 extension 
Organisation Government of Scotland 
Sector Public
Country United Kingdom
Start 09/2019 
End 09/2021
 
Description Whole Genome Sequencing for Health and Wealth Initiative
Amount £2,000,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 02/2016 
End 01/2018
 
Title Whole genome sequencing 
Description A whole genome sequencing facility was established in the University of Edinburgh. The facility has enabled collaborations locally and nationally including the sequencing of 14,000 whole genomes of humans and agricultural animals. The Pan-Scotland Scottish Genomes Partnership joined four Scottish medical schools, four regional genetic centres and their collaboration with Genomics England and the 100,000 Genomes Project. This included diagnostic testing by whole genome sequencing of more than 300 patients in the Scottish NHS and has led to £4.2 million of further funding for genome-based testing by the Scottish Government for patient care. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact The diagnostic rate of around 20-25% was realised for patients in the Scottish NHS. Major industrial collaborations were established for agricultural genomics to improve agricultural health and productivity. 
 
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
 
Description Long read sequencing in rare genetic disease 
Organisation Genomics England
Country United Kingdom 
Sector Public 
PI Contribution This is a pan Scotland with the four clinical genetics departments in Scotland and Genomics England. We have developed protocols for long read sequencing and are now analysing these for comparison with short read sequencing and other means of genetic investigation such as microarrays.
Collaborator Contribution Across Scotland, Clinical Geneticists have provided cases for the short read preliminary project that will feed into larger numbers for the long read project. Edinburgh Genomics, the University of Edinburgh genomics facility, have provided significant intellectual support and infrastructure for the project. Genomics England are research collaborators on methods for analysis
Impact Through this activity, the collaboration with Genomics England has continued to be active. A new collaboration with the University of Oxford has led to new diagnoses, two national presentations and a draft manuscript at the advanced stage of preparation.
Start Year 2022
 
Description Long read sequencing in rare genetic disease 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution This is a pan Scotland with the four clinical genetics departments in Scotland and Genomics England. We have developed protocols for long read sequencing and are now analysing these for comparison with short read sequencing and other means of genetic investigation such as microarrays.
Collaborator Contribution Across Scotland, Clinical Geneticists have provided cases for the short read preliminary project that will feed into larger numbers for the long read project. Edinburgh Genomics, the University of Edinburgh genomics facility, have provided significant intellectual support and infrastructure for the project. Genomics England are research collaborators on methods for analysis
Impact Through this activity, the collaboration with Genomics England has continued to be active. A new collaboration with the University of Oxford has led to new diagnoses, two national presentations and a draft manuscript at the advanced stage of preparation.
Start Year 2022
 
Description Long-read sequencing for diagnosis of rare disease 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Genetic data on cohort of patients with rare disease.
Collaborator Contribution Analytical expertise.
Impact Oral presentations to national meetings.
Start Year 2023
 
Description Scottish Genomic Medicine 
Organisation Genomics England
Country United Kingdom 
Sector Public 
PI Contribution The Scottish Genomes Partnership has been a major collaboration with Genomics England with sharing of genome data and diagnostic tests being carried out for over 1000 patients/family members from the Scottish NHS. Over £1 million in funding was awarded to continue whole genome sequencing of Scottish NHS patients by the scottish Government and further £3 million awarded through the Scottish NHS for exome-based testing of Scottish NHS patients.
Collaborator Contribution Genomics England have hosted and analysed the genome sequences and clinical information of Scottish genomes and returned categorised genomic variants of potential or actual diagnostic significance. New diagnoses on the SGP Extension funding have been made in a cohort of 250 new sequenced genomes. Initial analysis has yielded a diagnostic rate of 15% but further diagnoses are expected on more detailed analyses.
Impact The overall SGP project outputs have now been published in Hocking et al, European Journal of Human Genetics, 2022. PMID 36474026.
Start Year 2017
 
Description Single molecule sequencing in rare disease and cancer 
Organisation Oxford Nanopore Technologies
Country United Kingdom 
Sector Private 
PI Contribution Patients with rare disease and cancer, biomedical and analytical expertise.
Collaborator Contribution Sequencing reagents.
Impact New diagnoses made. Presentations to national meetings.
Start Year 2023
 
Description AdMedSci/RSE, Working together to address health challenges in Scotland, Edinburgh, Delegate 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Joint meeting of a AcMedSci and Royal Society of Edinburgh showcasing activities in common.
Year(s) Of Engagement Activity 2023
 
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 CRUK, CRUK Scotland Centre Annual Meeting, Glasgow, Delegate 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Annual meeting of Scotland's CRUK Cancer Centre.
Year(s) Of Engagement Activity 2023
 
Description CSO, Scotland's Health Research and Innovation Conference, 50 years of advancing healthcare, Glasgow, Delegate 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact A national showcase of precision medicine and other CSO activities for academic experts and experts from industry.
Year(s) Of Engagement Activity 2023
 
Description Cross-Party Group: Rare, Genetic and Undiagnosed Conditions, Edinburgh, "Genomic Medicine in Scotland - the Scottish Science Advisory Council Report" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Parliamentary cross-party group meeting. Presentation and discussion about national policy.
Year(s) Of Engagement Activity 2019
 
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 Facebook video presentation, liquid biopsy 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact In collaboration with Cancer Research UK I was filmed for a public engagement video to describe my research on liquid biopsy and its clinical implications. The video was posted on Facebook and received over 1 million views.
Year(s) Of Engagement Activity 2019
URL https://www.facebook.com/7950759473/posts/313130479345003
 
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 NHS, Scottish Inherited Metabolic Disease Interest Group (SIMDIG), Stirling, "Genome-based Genetic Testing" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact National metabolic diseases forum presentation.
Year(s) Of Engagement Activity 2019
 
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 Oxford Global, 17th Annual Biomarkers Congress, Manchester, Speaker "Liquid Biopsy Biomarker Development and Implementation for Precision Oncology" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Showcasing and networking actitivities in precision oncology.
Year(s) Of Engagement Activity 2023
 
Description Oxford Nanopore Technologies, Nanopore Community Meeting 2022, New York, USA, Speaker, "Long-read genome sequencing in Scottish patients with rare disease" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I was an invited speaker at this international meeting with an in-person and virtual audience of 4400. Excellent feedback from my talk, extensive opportunities for networking and future planning.
Year(s) Of Engagement Activity 2022
 
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
 
Description Royal Society of Scottish Arts Lectures, Edinburgh, "The Human Genome - its Scientific and Societal Impact" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Invited presentation to learned society.
Year(s) Of Engagement Activity 2019
 
Description School of Law, Legitimacy and Succession Roundtable, Edinburgh, "DNA and genetics explained" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Convened by the local school of law, senior lawyers and policy makers attended this invited workshop where the reportee was the genetics expert in presentation and discussion.
Year(s) Of Engagement Activity 2019
 
Description Scottish Biomedical Postdoctoral Researcher Conference, Glasgow, "The Roadmap to a National Programme in Genomic Medicine" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact This working group was organised by Cancer Research UK to develop a 10 year roadmap for its programme on early detection of cancer. Consultative presentations working group discussions fed into outline policy.
Year(s) Of Engagement Activity 2019
 
Description Scottish Genomics Leadership Group (SGLG), Government policy group, group member 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Expert contribution to national policy forum on genomics in medicine.
Year(s) Of Engagement Activity 2021,2022
 
Description Scottish Government, Stakeholder meeting with senior officials from PRECISE and Singapore's Ministry of Health, Glasgow, Speaker "Liquid biopsy for precision oncology in Scotland" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact A national showcase of precision medicine including experts from industry and international experts from the Far East.
Year(s) Of Engagement Activity 2023
 
Description UK Government Office for Life Sciences (OLS), UK genomics strategy discussion, Edinburgh. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact The UK Government Office for Life Sciences (OLS) has been drafting a UK genomics strategy in consultation with UK National Genomics Board (https://www.gov.uk/government/groups/national-genomics-board). Professor Aitman was an invited expert.
Year(s) Of Engagement Activity 2020
URL https://www.gov.uk/government/groups/national-genomics-board
 
Description UK Rare Diseases Forum, Edinburgh, "Rapid Whole Genome Sequencing" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact National meeting on genetics of rare diseases for a wide audience including policy makers, scientists, clinicians, funders. The meeting built collaborations from the research findings and clinical activity presented.
Year(s) Of Engagement Activity 2019
 
Description University of Edinburgh, AI and Biomedicine, Edinburgh, Delegate 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact High level strategy group for the University of Edinburgh to define strategic priorities for AI and biomedicine.
Year(s) Of Engagement Activity 2023
 
Description University of Edinburgh, Edinburgh Next Generation of Genomics Symposium (ENGoGS), Edinburgh, Speaker/Delegate 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Symposium for early career researchers and industry to showcase and develop strategy in genomic applications to healthcare, across species and disciplines.
Year(s) Of Engagement Activity 2023