Infrastructure for collaboration: Leeds MRC Medical Bioinformatics Centre

Lead Research Organisation: University of Leeds
Department Name: School of Medicine

Abstract

For some years medical research has been advanced by new technologies that generate very large amounts of biological data in digital format, for example, new methods that generate very detailed and often three-dimensional images of arthritic joints or new ways of sequencing DNA that bring information on inherited disease. Until recently many of these methods have been limited to research studies, clinical trials and small numbers of patients but recent advances mean that we can now contemplate a future where every individual may know their genome sequence, and where most people will have medical investigations that generate this type of data in routine practice.

In parallel to these developments, the UK NHS is increasingly moving away from using paper to store vital information about patient care and adopting modern computer systems which store patients' health records in a secure electronic format. These patient records are valuable data from which we can learn a great deal about the efficacy of health care and the long term effects of treatments. However, it is clear that the value of these health care records to research will be increased if they can be effectively linked to the large scale data described above. It will be possible for instance to make detailed investigations of how treatments may be better or worse depending on the genetics of the person receiving them, and help move towards a world of personalised medicine.

Bringing large amounts of varied and complex data from different sources is not without challenge. The data need to be accessible and usable by those with a broad range of backgrounds, including researchers familiar with using complex research data and clinicians familiar with accessing patient records. There are also issues around ethics and privacy, plus the development and sustainability of necessary powerful computing infrastructure to support the linking and secure sharing of data between NHS and research institutions.

We aim to overcome these challenges through the creation of the Leeds MRC Medical Bioinformatics Centre which will develop and sustain the infrastructure, experience and facilities needed to undertake ground-breaking research at the point where clinical, health and research data meet. This will be achieved by bringing together a strong team who between them have extensive experience spanning all aspects of the relevant areas including direct patient care, high performance computing, statistics, biomedical and health research. The Centre will build on established and successful links between the University of Leeds, the Leeds Teaching Hospital Trust (LTHT), an external company specialising in medical record systems (The Phoenix Partnership, (TPP)) and the Leeds-based NHS Health & Social Care Information Centre (HSCIC).

The Centre will bring together state of the art technology for visualising data and provide a hub for the training of future researchers in this rapidly developing and complex area. The computing infrastructure will be used to establish a Shared Virtual Datacentre (SVD) which will provide researchers with a highly secure and powerful computing platform.

The Centre will be set up over the first two years of this project, and will support an increasing number of research projects aiming directly at health care improvements. Initial projects will focus on inherited diseases (the genetic causes of neuro-developmental delay), kidney disease (detecting kidney injury before complications ensue), skin cancer (understanding what leads it to spread) and colorectal cancer (understanding the long term effects of surgery combined with radiotherapy). These projects will demonstrate the ways that our Centre will develop new insights into the factors that drive disease, and provide indicators that inform treatment leading to better, more personalised and more effective medicine and health care.

Technical Summary

The capital expenditure for the Leeds MRC Medical Bioinformatics Centre will complete an integrated Research Campus linking the University campus to the local Leeds Teaching Hospitals Trust (LTHT), The Phoenix Partnership Ltd (TPP) and HSCIC. This requires upgrades of some existing network links to 100 Gb/s, and extra data storage capability on the University Campus within the Yorkshire and Hull Metropolitan Area Network shared data centre. This is linked to matched funding for infrastructure within LTHT and TPP. Computational processing will be carried out on the University high-performance computing facility, free of direct cost to this application. Capital funds will also be used to refurbish part of a building (Worsley) to house the Centre and associated researchers. Non-capital costs will be met partly from University matched funding and are associated mainly with data scientists and high calibre research fellows. These staff will create and stress test Virtual Research Environment software specialised to the linkage of high-volume molecular (e.g. sequence) data and phenotypic data (e.g. pathology images) to appropriate anonymized health and clinical records. Stress testing will use exemplar projects in disease areas (inherited disease, melanoma, rectal cancer and renal injury) where we already have consented cohorts with significant genomic, proteomic and phenotypic data sets. A key aim of the Centre will be scientific and financial sustainability through the continued creation and funding of new projects based on the infrastructure and capability in place. Other important aspects of the centre will be work on ethics and appropriate electronic consent processes, patient and clinician communication, and engagement and education and training. We will set up and deliver a new MSc programme, a PhD training platform and engage with undergraduate teaching.

Planned Impact

We have developed a detailed plan for the achievement of social and economic impact of the MRC Centre which is provided in the 'Pathways to Impact' document. To summarise, we envision a project pathway model (Fig. 2 in the Case for Support) whereby research in medical bioinformatics is driven by clinical questions, and leads to excellent science that goes hand-in-hand with ultimate economic, societal and/or clinical impact. We have put in place a range of activities to support this model, and achieve the desired impacts. These include regular seminars, conferences and workshops addressing clinicians, industry and policy makers where the Centre's achievements, its methodology and its projects will be disseminated.

We recognise the key role to be played in our processes by the patients whose records and data we will use to drive research. It is critical to the impact of the Centre that large numbers of patients understand how their anonymised data can lead to research advances of societal and economic benefit, and that they consent to this. We will promote this through regular patient engagement meetings, and making the consent processes and software we will develop during the project as clear and user-friendly as possible.

Our communication plans are also described elsewhere. They include a highly functional, content-rich website, e-newsletters, social media and other communications activities. These will reach a diverse and wide range of stakeholders with messages in appropriate language tailored their interests.

Training and capacity development will be a major part of the Centre's activities, from undergraduates in medicine and other disciplines, Masters students on our subject specific courses, a large cohort of PhD students, research fellows and other professionals engaging in CPD activities (our modules are usually available in this format). This will produce a large number of well-trained professionals who will provide impact from academic research to small biotechnology companies and larger pharmaceutical companies.

Publications

10 25 50
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Abell TL (2015) Neurostimulation of the gastrointestinal tract: review of recent developments. in Neuromodulation : journal of the International Neuromodulation Society

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Abhyankar P (2014) Framing Options as Choice or Opportunity: Does the Frame Influence Decisions? in Medical decision making : an international journal of the Society for Medical Decision Making

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Absolom K (2015) Beyond lip service and box ticking: how effective patient engagement is integral to the development and delivery of patient-reported outcomes. in Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation

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Affleck P (2018) Sharing patient data: understanding anonymisation. in BMJ (Clinical research ed.)

 
Description Accelerated Access Review
Geographic Reach National 
Policy Influence Type Citation in other policy documents
Impact The Accelerated Access Review aims to increase the uptake of research innovations by the NHS, through a variety of novel interventions.
URL https://www.gov.uk/government/publications/accelerated-access-review-interim-report
 
Description Appointment Panel Member for Director of the National Institute for Health and Biomedical Informatics Research
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
URL https://www.mrc.ac.uk/about/institutes-units-centres/uk-institute-for-health-and-biomedical-informat...
 
Description Appoointed Board Member for the NIHR Clinical Researech Network Coordinating Centre
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact National recruitment to approved clinical trials approaching 1 million patients pa across the NHS.
URL https://www.nihr.ac.uk/explore-nihr/support/clinical-research-network.htm
 
Description Chairman, Joint Partnership Board, GeNEQ combined Northern and Yorkshire & Humber Genomic Medicine Centre, NHS England
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
URL https://www.genomicsengland.co.uk/about-genomics-england/the-100000-genomes-project/genomic-medicine...
 
Description Chairman, Office for the Strategic Co-ordination of Health Research (OSCHR) Health Informatics Group
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact Improved accessibility of electronic patient records for research purposes.
URL https://www.mrc.ac.uk/about/what-we-do/spending-accountability/oschr/
 
Description MRC Centre Director is a Non-Executive Director of Health Data Research UK.
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact It is anticipated that HDR-UK will have a major beneficial effect on medical research and health outcomes as a result of better analysis of patient datasets.
URL https://hdruk.ac.uk/
 
Description MRC Centre Director is a Non-Executive Director of UK Biobank
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact UK Biobank progressively impacts on our understanding of predisposing factors for disease in the UK population.
 
Description MRC Unit and Centre Portfolio Review, Main Panel Member
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact Optimisation of the portfolio (and hopefully the outputs and effectiveness) of the MRC's investment in its Units and Centres in the coming decade.
URL https://mrc.ukri.org/about/institutes-units-centres/
 
Description Presentation at MRC Open Council Meeting on 10th July 2014 on "Realising MRC's Vision in Health and Bioinformatics"
Geographic Reach National 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
Impact Attempt to illustrate that the MRC's policy in this important area of healthcare research (and its impact on the UK "health and wealth" agenda) is soundly based.
 
Description UseMYData.com
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact UseMYData.com is a successful and increasingly influential organisation enabling cancer patients in particular to bring pressure to bear so that their own health data can be used for research purposes.
URL http://www.usemydata.org/
 
Description Creating a UK Colorectal Cancer Intelligence Hub
Amount £3,200,000 (GBP)
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2017 
End 04/2022
 
Description Doctoral Training Programme in Discovery Medicine over the Lifecourse. MRC Doctoral Training Partnership
Amount £3,032,496 (GBP)
Funding ID MR/N013840/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 09/2016 
End 03/2022
 
Description EPSRC. [EP/N013980/1]. Quanticode: Intelligent infrastructure for quantitative, coded longitudinal data. £977,833. 2016-2019. R Ruddle (PI), AF Markham and 5 others.
Amount £977,833 (GBP)
Funding ID EP/N013980/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 01/2016 
End 01/2019
 
Description Health Data Research UK, UK Research and Innovation Industrial Strategy Challenge Fund/Rutherford Fund Fellowships, Dr A P Droop and C M Carrigan
Amount £655,634 (GBP)
Organisation Health Data Research UK 
Sector Private
Country United Kingdom
Start 02/2018 
End 03/2021
 
Description Healthcare Impact Partnerships 2016. Microbubble Enhanced Imaging and Therapeutic Delivery
Amount £822,232 (GBP)
Funding ID EP/P023266/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 06/2017 
End 06/2020
 
Description MRC Clinical Research Infrastructure Initiative
Amount £7,625,237 (GBP)
Funding ID MR/M008991/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start  
 
Description MRC Clinical Research Infrastructure Initiative: Single Cell Functional Genomics Centre
Amount £1,139,000 (GBP)
Funding ID MR/M009084/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start  
 
Description MRC Populations and Systems Medicine Board: Treatment according to response in Giant Cell Arteritis (TARGET)
Amount £700,000 (GBP)
Funding ID MR/N011775/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 11/2015 
 
Description Prof Julia Newton-Bishop et al, Programme Grant: Using tumour, peripheral blood and sentinel nodal transcriptomics to understand the interaction between melanomas and the host
Amount £953,389 (GBP)
Funding ID MR/M019012/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 06/2015 
End 05/2020
 
Description Sir Henry Wellcome Postdoctoral Fellowship, Dr Marlous Hall
Amount £565,000 (GBP)
Funding ID 206470/Z/17/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2017 
End 09/2021
 
Title Bioinformatics Software Development 
Description Novel software for bioinfomatic analysis. qsubsec: a lightweight template system for defining sun grid engine workflows. Droop AP. Bioinformatics. 2015 Dec 3. pii: btv698. [Epub ahead of print]. 
Type Of Material Improvements to research infrastructure 
Year Produced 2015 
Provided To Others? Yes  
Impact To be determined. 
URL http://bioinformatics.oxfordjournals.org/content/early/2015/12/25/bioinformatics.btv698.long
 
Title Bioinformatics Software Development 
Description Sequence analysis: fqtools: An efficient software suite for modern FASTQ file manipulation Alastair P. Droop1,* 1MRC Medical Bioinformatics Centre, University of Leeds, Clarendon Way, Leeds, LS2 9NL, UK Published in the journal Bioinformatics, 18th February 2016. 
Type Of Material Improvements to research infrastructure 
Year Produced 2016 
Provided To Others? Yes  
Impact Already extensively cited. 
URL https://bioinformatics.oxfordjournals.org/content/early/2016/02/18/bioinformatics.btw088.full.pdf?ke...
 
Title Leeds Integrated Research Campus 
Description A secure computing environment, ISO 27001 and NHS Digital IG Toolkit compliant. Information Security Management Systems: See for example, https://workspace.leeds.ac.uk/sites/IRC/Workflow/_layouts/15/WopiFrame.aspx?sourcedoc=/sites/IRC/Workflow/Shared%20Documents/ISMS%20Polices%20and%20Procedures/IRC%20Framework%20of%20the%20Information%20Security%20Management%20System.docx?tion=default https://workspace.leeds.ac.uk/sites/IRC/Workflow/_layouts/15/WopiFrame.aspx?sourcedoc=/sites/IRC/Workflow/Shared%20Documents/ISMS%20Polices%20and%20Procedures/IRC%20Framework%20of%20the%20Information%20Security%20Management%20System.docx?tion=default https://workspace.leeds.ac.uk/sites/IRC/Workflow/_layouts/15/WopiFrame.aspx?sourcedoc=/sites/IRC/Workflow/Shared%20Documents/ISMS%20Polices%20and%20Procedures/IRC%20Framework%20of%20the%20Information%20Security%20Management%20System.docx?tion=default https://workspace.leeds.ac.uk/sites/IRC/Workflow/_layouts/15/WopiFrame.aspx?sourcedoc=/sites/IRC/Workflow/Shared%20Documents/ISMS%20Polices%20and%20Procedures/IRC%20IS%20Audit%20and%20Management%20Procedure.docx?tion=default https://workspace.leeds.ac.uk/sites/IRC/Workflow/_layouts/15/WopiFrame.aspx?sourcedoc=/sites/IRC/Workflow/Shared%20Documents/ISMS%20Polices%20and%20Procedures/ITEnvironmentAndInfrastructureSOP.docx?tion=default https://workspace.leeds.ac.uk/sites/IRC/Workflow/_layouts/15/WopiFrame.aspx?sourcedoc=/sites/IRC/Workflow/Shared%20Documents/ISMS%20Polices%20and%20Procedures/IRC%20User%20Agreement.docx?tion=default https://workspace.leeds.ac.uk/sites/IRC/Workflow/_layouts/15/WopiFrame.aspx?sourcedoc=/sites/IRC/Workflow/Shared%20Documents/ISMS%20Polices%20and%20Procedures/IRC%20ISMS%20Documentation%20Overview.docx?tion=default 
Type Of Material Improvements to research infrastructure 
Provided To Others? No  
Impact The secure data environment provided through the IRC is designed to persuade data custodians that it is safe to share their data for analysis (with appropriate consents, levels of anonymisation, Section 251/CAG approvals and ethical permissions) with approved researchers. 
URL http://lida.leeds.ac.uk/about-lida/integrated-research-campus/
 
Title The LTHT Patient Pathway Management System 
Description The PPM system is the Electronic Patient Care Record of the Leeds Teaching Hospitals NHS Trust. Access to confidential material in this record is provided to the Leeds MRC Centre by the LTHT. This is one of the largest secondary care EPRs in the UK (from the second largest NHS acute trust). 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Many of the outputs in the "Publications" section are from members of the MRC Centre with LTHT clinical contracts, who routinely use PPM in their research. 
 
Title The Leeds Integrated Research Campus (IRC). Achieved full ISO 27001 and NHS Digital IG Toolkit accreditation in 2017 
Description The shared computing and secure data storage infrastructure provided by the MRC and ESRC awards funding the Leeds MRC Medical Bioinformatics Centre and the ESRC Consumer Data Research Centre. Collectively, this comprises the Leeds Institute for Data Analytics (LIDA). 
Type Of Material Data handling & control 
Year Produced 2015 
Provided To Others? Yes  
Impact Extensive new interdisciplinary research activities across all the Faculties in the University of Leeds. Links to external partner organisations: HSCIC, LTHT, CPRD, TPP, EMIS, Leeds City Council. 
URL http://www.lida.leeds.ac.uk/
 
Description Clinical Practice Research Datalink 
Organisation Medicines and Healthcare Regulatory Agency
Department Clinical Practice Research Datalink (CPRD)
Country United Kingdom 
Sector Public 
PI Contribution The MRC Centre Director is Chair of the CPRD Expert Advisory Group. As a non-Executive Director of the MHRA, the MRC Centre Director takes particular responsibility for oversight of the activities of the CPRD for the Agency Board. The Director was reappointed to the Board of MHRA in 2016 and has been invited to serve a third term of office in 2019.
Collaborator Contribution CPRD is to be a supplier of linked datasets to the MRC Centre under an annual licence agreement.
Impact The MRC Centre Director facilitates the relationship between CPRD and the HSCIC, by advising the CPRD Dirtector. The Centre Director continues in this role with the formation of NHS Digital. The MRC Centre Director was a member oif the appointment committee for the new CPRD Director in 2015. He sat on a Civil Service promotions committee for Dr Valentine in 2018.
Start Year 2014
 
Description EMIS Egton Medical Information Systems 
Organisation EMIS Group
Country United Kingdom 
Sector Private 
PI Contribution Major supplier of software systems to GPs in the UK. Exchange of information with the Leeds MRC Medical Bioinformatics Centre on potential improvements to their systems. For example, in February 2016, suggested that they should include an MHRA compliant "Yellow Card" capability in their GP system to facilitate reporting of adverse drug reactions.
Collaborator Contribution EMIS provides software support to MRC Centre investigators in the Leeds Teaching Hospitals NHS Trust. For example, the LTHT adult Cystic Fibrosis patients are managed with a hospital EHR based on the EMIS platform.
Impact The Leeds MRC Medical Bioinformatics Centre Director advises the Board of EMIS and the EMIS Chairman, Dr Michael O'Leary, on strategic issues facing the Company. Under the auspices of the MRC Centre, EMIS and the LTHT Informatics Director are exploring options for joint development of interfaces between the hospital electronic patient record (PPM+) and the EMIS primary care software product. The new CEO of EMIS, Andy Thorburn, is also a member of the OSCHR Health Informatics Group. The MRC Centre Director has been influential in persuading EMIS to flow data into CPRD and latterly UK Biobank. Good links have been established now between EMIS and Health Data Research UK.
Start Year 2015
 
Description ESRC Consumer Data Research Centre 
Organisation Economic and Social Research Council
Department ESRC CDRC
Country United Kingdom 
Sector Academic/University 
PI Contribution The Leeds MRC Medical Bioinformatics Centre and Leeds ESRC Consumer Data Research Centre share accommodation and facilities. There are extensive interdisciplinary research collaborations.
Collaborator Contribution The ESRC CDRC contributes to our activities through our joint creation of a cross-faculty collaboration, The Leeds Institute for Data Analytics.
Impact Multi-disciplinary partnership. One success this year has been the award of a substantial grant to LIDA from the EPSRC. EPSRC. [EP/N013980/1]. Quanticode: Intelligent infrastructure for quantitative, coded longitudinal data. £977,833. 2016-2019. R Ruddle (PI), AF Markham and 5 others. The core ESRC Grant for the Consumer Data Research Centre in LIDA was renewed in 2018.
Start Year 2014
 
Description HSCIC Links. Modified in 2016 on change of name to NHS Digital 
Organisation Health & Social Care Information Centre (HSCIC)
Country United Kingdom 
Sector Public 
PI Contribution The MRC Centre Director has helped co-ordinate the activities of the HSCIC and MRC at Board level, where their interests overlap. The MRC Centre Director is a member of the Academic Advisory Group to the HSCIC Board. THe MRC Centre Director has served as a member of the NHS Digital Research Advisory Group since its creation (2016-date). The MRC Centre Director is a member of the NHS Digital Consent Working Group. The Director works closely with the new CEO of NHS Digital (Sarah Wilkinson) and mentors members of her Senior Leadership Team. He is also consulted by the Chair of NHS Digital, Noel Gordon. An MRC Centre Senior Fellow (Chris Carrigan) has chaired the NHS Digital independent Group Advising on the Release of Data (iGARD).
Collaborator Contribution HSCIC is a supplier of linked data to the MRC Centre. NHS Digital is an enthusiastic contributor to the work of the OSCHR Health Infromatics Group, chaired by the MRC Centre Director. This OSCHR Group has been influential in shaping the so-called "GP Systems of Choice" re-procurement in 2018-19.
Impact MRC Centre Director provides ad hoc advice to the Chief Executive and Caldicott Guardian of the HSCIC (and now NHS Digital).
Start Year 2014
 
Description Health Data Research UK 
Organisation Health Data Research UK
Country United Kingdom 
Sector Private 
PI Contribution I was appointed as a Non-Executive Board Director of HDR UK in 2017. I chair the HDR UK Audit and Risk Committee. I sat on the appointment committee for the Director of HDR UK. I am Convenor of a process to establish a joint British Heart Foundation/HDR UK Cardiovascular Data Science Centre (initial 5 year indicative budget £5m). I am the only clinician on the Board of HDR UK.
Collaborator Contribution Leadership of the UK health data research agenda from which the Leeds MRC Centre benefits indirectly. Much more important is that all the collaborations across the data custodians' landscape established by this MRC Centre are made freely available to HDR UK. Although this Board appointment began in 2017, the MRC Centre Director was heavily involved in the eventual creation of HDR UK with MRC colleagues and the Farr Institute from 2015 onwards.
Impact The Health Data Research Alliance https://www.hdruk.ac.uk/digital-innovation-hubs/uk-health-data-research-alliance/ BHF/HDR UK Cardiovascular Data Science Centre https://www.bhf.org.uk/what-we-do/news-from-the-bhf/news-archive/2019/october/millions-of-patients-to-benefit-from-10m-national-cardiovascular-data-science-centre
Start Year 2017
 
Description Leeds Institute for Data Analytics http://lida.leeds.ac.uk/ 
Organisation Economic and Social Research Council
Department ESRC CDRC
Country United Kingdom 
Sector Academic/University 
PI Contribution MRC Medical Bioinformatics Centre and the ESRC Consumer Data Research Centre in Leeds share interdisciplinary research accommodation, research facilities and computing resources (the Leeds "Integrated Research Campus", IRC). This core computing resource and much of our shared refurbished accommodation was funded through the MRC Centre capital award. The General Manager of the MRC Medical Bioinformatics Centre (Mr Adrian Iredale, funded through the MRC award), also acts as the General Manager of LIDA.
Collaborator Contribution Research opportunities arising from the ability to analyse population health and behavioural data in an integrated secure computing environment.
Impact Numerous multidisciplinary grant applications and research projects. Combined EOI submitted to MRC for consideration in the new National Institute for Health and Biomedical Informatics Research. In 2018, the University of Leeds paid its contribution to become a full member of the Alan Turing Institute (EPSRC). This membership is managed scientifically through LIDA.
Start Year 2015
 
Description Leeds Teaching Hospitals NHS Trust (LTHT) Collaboration 
Organisation Lithotech Group
Country Israel 
Sector Private 
PI Contribution £1,135,792. LTHT provides access (under conditions of strict patient confidentiality) to electronic patient records, for approved and accredited researchers in the Leeds MRC Medical Bioinformatics Centre. This has involved provision of additional data storage and extraction capacity within the LTHT NHS firewalls. The first analyses of these data sources have commenced.
Collaborator Contribution LTHT is responsible for maintaining the confidentiality of the electronic records of all its patients and obtaining and recording the existence of appropriate consent for research uses. Without the contribution of our partner NHS Trust, the MRC Centre simply could not function.
Impact Many of the investigators on this award hold honorary clinical contracts with the LTHT. Their published outputs are included in the "Publications" section.
Start Year 2014
 
Description MRC Centre for Drug Safety Science, University of Liverpool 
Organisation University of Liverpool
Country United Kingdom 
Sector Academic/University 
PI Contribution The MRC Medical Bioinformatics Centre Director is Chairman of the CDSS Scientific Advisory Board.
Collaborator Contribution Under Prof Sir Munir Pirmohamed's direction, the Leeds MRC Centre Director contributes to the UK Pharmacogenetics and Stratified Medicine Network.
Impact Assisted in the CDSS achieving excellence in its activities. The process of appying for ongoing MRC funding for the CDSS in 2019 has just begun, with the full support of the Scientific Advisory Board.
Start Year 2014
 
Description NERC National Centre for Atmospheric Science 
Organisation National Centre for Atmospheric Science (NCAS)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Providing ad hoc medical research advice to the Director of NCAS in Leeds, Prof Stephen Mobbs.
Collaborator Contribution Access to atmospheric pollution/air quality data for joint grant applications for the study of the impact of air quality on human health.
Impact Multi-disciplinary (medicine, earth sciences, geography, social sciences).
Start Year 2015
 
Description The Poenix Partnership (TPP) 
Organisation TAP Biosystems
Country United Kingdom 
Sector Private 
PI Contribution TPP is a major supplier of software systems to primary care across the UK. In our region, approximately 80% of GPs use TPP. TPP has developed a research dataset (ResearchOne) based on its routine clinical information platform, SystmOne. Access to this dataset is essential for the analytical research conducted in the MRC Centre. The development of this collaboration has been funded in the past by the UK Technology Strategy Board.
Collaborator Contribution Provision of access to the ResearchOne dataset. As a result of this collaboration, a new collaboration between TPP and the LTHT has been established.
Impact Many of the Investigators in the Leeds MRC Centre have ongoing collaborations with TPP. Where publications have arisen as a result, these are included in the "Publications" section. TPP have also been enthusiastic participants in the OSCHR Health Informatics Group, chaired by the MRC Centre Director. Through this, pressure has been applied to (eventually) achieve flows of TPP data into key national datasets, particularly UK Biobank and CPRD.
Start Year 2014
 
Title Innovate UK Medicines Discovery Catapult. Director of the MRC Medical Bioinformatics Centre is a Founding Board Member 
Description The Medicines Discovery Catapult exists to support UK SMEs in developing new medical interventions. It catalyses interactions between SMEs and academic researchers. It has strong links and collaborations with Life Arc, the former MRC Technology Transfer arm. It is now funded by Innovate UK until 2023 in the first instance. 
Type Therapeutic Intervention - Drug
Current Stage Of Development Initial development
Year Development Stage Completed 2016
Development Status Under active development/distribution
Impact The Medicines Discovery Catapult has already changed the landscape for early drug discovery at the academic/SME interface in the UK. It also has an ongoing activity in the applications of advanced IT-based approaches in the drug discovery process. https://md.catapult.org.uk/resources/use-of-health-data-by-the-life-sciences-industry-a-uk-perspective/ It has also become highly influential in shaping national policies in medicnes research. 
URL https://md.catapult.org.uk/
 
Description ACCELERATED ACCESS REVIEW: EXTERNAL ADVISORY GROUP 
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 Leeds MRC Medical Bioinformatics Centre Director is a Member of the External Advisory Group for the Accelerated Access Review, convened by the Minister, George Freeman MP.

This Group has met several times in 2015 and 2016. The Interim Report URL is below.
Year(s) Of Engagement Activity 2015,2016
URL https://www.gov.uk/government/publications/accelerated-access-review-interim-report
 
Description Director of the MRC Medical Bioinformatics Centre is a Non-Executive Director of the MHRA 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The MRC Medical Bioinformatics Centre Director is the Medicines and Healthcare Products Regulatory Agency (MHRA) Non-Executive Director with specific Board responsibilities for the Clinical Practice Research Datalink (CPRD).
Year(s) Of Engagement Activity 2014,2015,2016,2017,2018,2019
URL https://www.cprd.com/intro.asp
 
Description Expert Advisory Group member, Connected Health Cities DH Programme 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact "Connected Health Cities" is a £20 million 3 year Department of Health/ NHSE Programme to facilitate research using healthcare data across the territories of the 4 North of England AHSNs. Monitoring performance against this budget is important to ensure optimal results.
Year(s) Of Engagement Activity 2015,2016,2017,2018
URL https://www.connectedhealthcities.org/
 
Description Farr Institute International Conference 2015, St Andrews, 26 - 28 August 2015 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Attended MRC "Big Data" Policy Meetings.
Delivered lecture to international audience on Big Data applications in Clinical Genetics.
Year(s) Of Engagement Activity 2015
 
Description Live@Leeds Symposium. Biomedical Informatics Meeting jointly with the UCL MRC eMedLab Centre 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Joint Symposium organised by 2 of the MRC Medical Bioinformatics Centres but drawing an audience of participants from across the UK and overseas.
Year(s) Of Engagement Activity 2016
 
Description MRC Postdoc Fellows Symposium 13 May 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presntation to all MRC clinical and non-clinical Fellows at their annual meeting.
Year(s) Of Engagement Activity 2015
 
Description Meeting with the Director of the MRC Farr Institute 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Workshop with Prof Andrew Morris on 11th July 2014 to ensure that the activities of the Leeds MRC Medical Bioinformatics Centre are fully integrated and co-ordinated with the activities of the Farr Instirute.

We have agreed to maintain and extend our dialogue with the Farr Institute. Further meetings have taken place with the Farr Institute centres in Manchester and at UCL.
Joint publications with the UCL Centre are included in the "Publications" section.
Year(s) Of Engagement Activity 2014
 
Description Meeting with the MRC Stratified Medicine Initiative Consortia 24th November 2015 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Meeting between the MRC Stratified Medicine Consortia and the members of the National Health and Biomedical Informatics Institute (Farr and Medical Bioinformatics Centre Directors) to define solutions to data management challenges in Consortia studies.
Year(s) Of Engagement Activity 2015
 
Description NIHR Senior Investigators Annual Meeting 3-4th November 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conveeened and presented in a "Big Data and Clinical Research - Panel Session".
Year(s) Of Engagement Activity 2015
 
Description National Health and Biomedical Informatics Institute Scientific Leaders' Roundtable, 30th November 2015 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact New group of national and international opinion leaders shaping the national agenda in health and biomedical informatics.
Year(s) Of Engagement Activity 2015
 
Description The MRC Medical Bioinformatics Centre Director is a member of the National Genomics Board, appointed by the Under-Secretary of State for Health, Lord OShaughnessy. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The newly formed National Genomics Board (2018) has a remit to oversee the work of the NHSE Genomic Medicine Centres.
Year(s) Of Engagement Activity 2018
 
Description eMedLab Symposium 14th January 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact eMedLab is an MRC-funded collaboration between Europe's leading biomedical scientists, involving UCL, the Francis Crick Institute, King's College London, the London School of Hygiene and Tropical Medicine, Queen Mary University of London, the Sanger Institute, and the EMBL European Bioinformatics Institute. Our objective is to maximise the gains for patients and for medical research that will come from the explosion in human health data. To realise this potential we need to accumulate medical and biological data on an unprecedented scale and complexity, to store it safely and securely, and to make it readily available to interested researchers for detailed analysis.



To this end, eMedLab and its partners are organising a meeting next year that will bring together prominent figures in the use of human health data. They will come from eMedLab, from its seven partners, and from other interested parties including the Farr Institute, Genomics England and the Alan Turing Institute. The meeting will feature presentations from some of the eMedLab career development fellows, together with short talks from leaders in the field of eHealth and medical bioinformatics. It will also offer the opportunity for informal conversations that will allow participants to discuss the future of research using human health data. A summary of the meeting will be published on the eMedLab website.
Year(s) Of Engagement Activity 2016
URL http://www.emedlab.ac.uk/