BREATHE - The Health Data Research Hub for Respiratory Health Capital Award
Lead Research Organisation:
University of Edinburgh
Department Name: UNLISTED
Abstract
What is the problem?
Everyone in the UK will have a respiratory illness at some point in their life. We have the best datasets in the world – which should be used to improve respiratory health – but these are currently very difficult to find, access and use.
What do we want to do?
People in the UK deserve the best respiratory health. We want to make respiratory health better by changing the way the NHS, pharmaceutical companies, charities and researchers use data.
How will we do it?
We will continue to develop BREATHE (the health data research hub for respiratory health) where trained, approved experts can access respiratory data to benefit patients and the public. We will make it easier for experts to use data in safe and secure ways.
How will this benefit patients?
BREATHE will support high quality research and cutting-edge innovation that will improve the lives of people living with respiratory conditions in the UK. It is important that patients and the public are involved with this project throughout, including from the very start. This is why there are patient and public members living with respiratory conditions who have worked with us on developing BREATHE and who are committed to delivering BREATHE’s goals.
Everyone in the UK will have a respiratory illness at some point in their life. We have the best datasets in the world – which should be used to improve respiratory health – but these are currently very difficult to find, access and use.
What do we want to do?
People in the UK deserve the best respiratory health. We want to make respiratory health better by changing the way the NHS, pharmaceutical companies, charities and researchers use data.
How will we do it?
We will continue to develop BREATHE (the health data research hub for respiratory health) where trained, approved experts can access respiratory data to benefit patients and the public. We will make it easier for experts to use data in safe and secure ways.
How will this benefit patients?
BREATHE will support high quality research and cutting-edge innovation that will improve the lives of people living with respiratory conditions in the UK. It is important that patients and the public are involved with this project throughout, including from the very start. This is why there are patient and public members living with respiratory conditions who have worked with us on developing BREATHE and who are committed to delivering BREATHE’s goals.
Technical Summary
Approximately 12.7 million people report a history of long-standing respiratory illness and respiratory disorders are the third leading cause of death. Lung diseases account for 10% of all inpatient bed-days, cost the NHS £11billion/year and society over £70billion/year. Despite having the richest respiratory datasets in the world, data are fragmented, inconsistently structured and cumbersome to access, severely limiting their utility.
Our vision is to transform the UK’s respiratory health through creating Findable, Accessible, Interoperable and Reusable (FAIR) respiratory rich datasets; providing expert support to catalyse their responsible use in respiratory research and innovation. We will position the UK at the forefront of data driven innovation; creating a ‘one-stop’ service for trustworthy, multi-stakeholder utilisation of curated respiratory data for public, private and third sector benefit. Our UK-wide consortium provides the necessary expertise. Our priorities have been co-developed with patients, the public, industry and med-tech partners; together we have identified
major opportunities for early, high-profile, case studies.
This capital award is to support continuing development of the BREATHE respiratory data platform. New data assets will be made available to the UK Health Data Research (HDR) Alliance and through the HDR Research Innovation Gateway. We will continue to develop a UK Respiratory Data Library (with metadata catalogue), curate and link data, and provide open-source algorithms to support secure analyses thereby enhancing the interoperability of datasets. This expandable platform will for example, enable the incorporation of data from wearable sensors into NHS apps to transform respiratory health, supporting rapid evaluation of new drugs and devices in real-world settings, and yielding evidence to underpin policy initiatives.
BREATHE will support stakeholders to securely use data to meet their diverse needs. We will work proactively with other Digital Innovation Hubs (DIH) to enhance the UK’s competitiveness.
Our vision is to transform the UK’s respiratory health through creating Findable, Accessible, Interoperable and Reusable (FAIR) respiratory rich datasets; providing expert support to catalyse their responsible use in respiratory research and innovation. We will position the UK at the forefront of data driven innovation; creating a ‘one-stop’ service for trustworthy, multi-stakeholder utilisation of curated respiratory data for public, private and third sector benefit. Our UK-wide consortium provides the necessary expertise. Our priorities have been co-developed with patients, the public, industry and med-tech partners; together we have identified
major opportunities for early, high-profile, case studies.
This capital award is to support continuing development of the BREATHE respiratory data platform. New data assets will be made available to the UK Health Data Research (HDR) Alliance and through the HDR Research Innovation Gateway. We will continue to develop a UK Respiratory Data Library (with metadata catalogue), curate and link data, and provide open-source algorithms to support secure analyses thereby enhancing the interoperability of datasets. This expandable platform will for example, enable the incorporation of data from wearable sensors into NHS apps to transform respiratory health, supporting rapid evaluation of new drugs and devices in real-world settings, and yielding evidence to underpin policy initiatives.
BREATHE will support stakeholders to securely use data to meet their diverse needs. We will work proactively with other Digital Innovation Hubs (DIH) to enhance the UK’s competitiveness.
| Description | Future of EAVE II and infrastructure for near real-time healthcare data access for research in Scotland |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | The Chief Scientist Office has continued to lead high level discussions with Scottish Government and NHS colleagues about the major benefits of using near real-time healthcare data in research beyond the acute phase of the COVID-19 pandemic. These discussions have continued and are being prioritised despite a change in the Chief Scientist for Health during this period. The Chief Scientist Office agrees that there is a key need for ongoing health surveillance permissions and infrastructure in Scotland, to support policymaking around areas such as other infectious diseases, other health hazards, antimicrobial resistance and non-communicable diseases of major health burden, as well as to provide ongoing whole system intelligence on the Scottish health and care system. |
| Description | Core Funding National Programme Award |
| Amount | £5,038,262 (GBP) |
| Funding ID | HDRUK2023.0027 |
| Organisation | Health Data Research UK |
| Sector | Private |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2028 |
| Title | Creation of respiratory registries in England, Wales, Scotland and Northern Ireland |
| Description | Curation of code and cohort profiles for COPD, ILD and asthma in primary and linked secondary care data in England (CPRD), Wales (SAIL), Scotland (DataLoch) and Northern Ireland (Honest Broker Service; not ILD yet). Specific details to be added to the Research Datasets impact tab when publication is complete. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Algorithms and code are reproducible as a research-ready resource and an improvement in data for industry, charity, academic and NHS use. This will enable a wider range of researchers to access data and code in a way that saves time/resource and ensures consistency in analyses and reporting. Initial use has been to describe the changing epidemiology of asthma, COPD and ILD between 2004 and 2023. Use of EHRs improves understanding of the evolving impacts of these disease on individuals, and the associated burden in the UK nations. |
| Title | How to create SNOMED CT codelists for primary care EHRs |
| Description | An entry in github breaks down the creation of SNOMED CT codelists into 9 steps. Example STATA, R and Python code is given for a smoking codelist for CPRD Aurum (but can be applied to any database using SNOMED CT codes). |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Publication in press. Impact will follow. |
| URL | https://github.com/NHLI-Respiratory-Epi/SNOMED-CT-codelists |
| Title | How to create drug codelists for recorded prescriptions |
| Description | An entry in github adapts the creation of SNOMED CT codelists, with considerations specific to generating codelists for drugs or medical devices, instead of for symptoms and conditions. The 9 steps are clearly described in a flow chart. Example STATA code is given. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Publication in press. Impact will follow. |
| URL | https://github.com/NHLI-Respiratory-Epi/drug-codelist-creation |
| Title | How to find acute exacerbation of COPD events in UK primary care EHRs |
| Description | An entry in github explains how an AECOPD can be found in primary care EHRs. Example STATA code is given. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Publication in press. Impact to follow. |
| URL | https://github.com/NHLI-Respiratory-Epi/AECOPD |
| Title | Sharing respiratory disease code on github |
| Description | By sharing and harmonising methodology for curating research-ready (and non-project-specific) datasets for these diseases across different electronic health record (EHR) databases in the UK, and generating consistent phenotype and variable definitions regardless of coding system, we aim to speed up research into respiratory diseases: Asthma, Interstitial Lung Disease (ILD) and Chronic Obstructive Pulmonary Disease (COPD). The EHR databases utilised in this project were the Clinical Practice Research Datalink (CPRD) Aurum for England; Secure Anonymised Information Linkage (SAIL) Databank for Wales; and DataLoch for South-East Scotland. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Publication is in press. Impacts will be reported in due course. |
| URL | https://github.com/NHLI-Respiratory-Epi/Curation-Harmonisation |
| Title | DataLoch Respiratory Registry |
| Description | This registry brings together data about South-East Scotland residents with acute and chronic respiratory conditions, specifically COPD (Chronic Obstructive Pulmonary Disease), asthma and ILD (Interstitial Lung Disease). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Proposals for use of these data are under review through the DataLoch application process. |
| URL | https://dataloch.org/data/about-the-data |
| Description | Collaboration with EXCEED |
| Organisation | University of Leicester |
| Department | Department of Epidemiology and Public Health |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Partnership with the SAIL Databank includes project set up, disclosure control output reviews, data loading and data checks, licenses, technical support, LINUZ and HPC costs. |
| Collaborator Contribution | Establish a project to develop and test capacity for TRE-based respiratory genomics data research, with a view to developing on initiatives like DARE-UK, PRUK, UKLLC and the HDR UK multi omics initiative. Contributions included enhancing the EXCEED study SAIL deposit with imported genomic data, alongside health linkages and lung function data; establishing a large-scale genomic research platform; testing and improving the SAIL respiratory genomic TRE with suitable research projects; adding new genomic, proteomic and metabololomics data; and expanding testing of the SAIL respiratory genomic TRE. |
| Impact | Capital funding from MRC led to setting up the SAIL Databank virtual machine with relevant statistical genetic software; preparing the respiratory genome-wide association study exemplars in EXCEED; generating the new genomic, proteomic, metabolomic and glycomic data; new data linkage; running respiratory statistical genetic analyses using the new data platform. |
| Start Year | 2022 |
| Description | Collaboration with QUB & Honest Broker Service |
| Organisation | Queen's University Belfast |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Professor Jenni Quint has shared code lists and algorithms to ensure consistency across datasets. Chris Orton has supported with technical aspects from SAIL. |
| Collaborator Contribution | Dialogue with the General Practitioner Intelligence Platform (GPIP), facilitation of data linkage with the Honest Broker Service and further data processing to build a respiratory cohort and derive variables to be used for future projects. |
| Impact | Capital funding from MRC enabled the first use of GPIP to build a cohort of patients with airway disease that can be used for research. The data are linked through the Northern Ireland Honest Broker Service to several other healthcare datasets including medication dispensing, emergency department contacts, hospital admissions and laboratory data to provide a unique linked dataset within Northern Ireland. Cohort definitions are based on Quality and Outcomes Framework registers for asthma and COPD, with code lists and variable definitions aligned to other UK nations for interoperability. Several respiratory research projects are planned as part of the HDRUK Inflammation and Immunity Programme, and a framework for future linkage in other disease areas within Northern Ireland. |
| Start Year | 2022 |
| Description | Collaboration with SAIL Databank |
| Organisation | SAIL Databank |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Chris Orton supported extension of the relationship with the SAIL Databank, to support further novel data linkages and development of analytical capacity for several BREATHE capital projects. |
| Collaborator Contribution | Project set up, disclosure control output reviews, data loading and data checks, licenses, technical support, LINUX and HPC costs. |
| Impact | Capital funding from MRC led to setting up the SAIL Databank virtual machine with relevant statistical genetic software; preparing the respiratory genome-wide association study exemplars in EXCEED; generating the new genomic, proteomic, metabolomic and glycomic data; new data linkage; running respiratory statistical genetic analyses using the new data platform. |
| Start Year | 2022 |
| Description | Met Office data |
| Organisation | Meteorological Office UK |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Participation in HDR UK visit to Met Office in October 2023, which introduced the Inflammation and Immunity Driver Programme and discussed synergies / opportunities for joint working based on consistently curated respiratory data in all 4 nations of the UK. Consistently curated respiratory data prepared through BREATHE is a foundation for this work. |
| Collaborator Contribution | Some options for joint projects / new linkage opportunities have been presented to Met Office staff and we are awaiting a response. |
| Impact | Currently at exploration stage |
| Start Year | 2023 |
| Description | Celebrating 10 years of the EXCEED study |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | In 2023, the EXCEED Study: a study of Genes, Environment and Health celebrated its 10th anniversary. To mark this special occasion, a series of 10 podcasts were recorded with Professor Turi King, and researchers who have used the EXCEED cohort to investigate a range of research questions. The series covers a broad range of topics including: lung function impairment, dynamic consent, the genetics of COVID-19, fatty liver disease, abdominal aortic aneurysm, personalised exercise, thyroid disease, treatment resistant depression and cough as a side effect of blood pressure treatment. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://citizen.le.ac.uk/podcasts/exceed/ |
| Description | EXCEED 10th Year anniversary event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Study participants or study members |
| Results and Impact | The EXCEED study - Extended Cohort for E-health, Environment and DNA - looks at the causes of long-term health conditions by collecting information about genes and lifestyle. A celebratory event was held to mark the 10-year anniversary of this major health study, which has recruited 11,000 patients across the county. It brought together research participants from across Leicester, Leicestershire and Rutland, as well as the public, with healthcare workers and scientists, to highlight the findings of nine of the 54 studies undertaken as part of EXCEED. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://le.ac.uk/news/2023/august/exceed |
| Description | HDR UK Board meeting: Science and Infrastructure Showcase |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The intended purpose of the meeting was to demonstrate impact from HDR UK support, in the form of research that institutions cannot do by themselves and encouraging early adoption. Prof Sir Aziz Sheikh gave a presentation on "Data-enabled Responses to Policy and Delivery Challenges". He explored the need for learning healthcare systems; talked about real-world delivery of data-enabled responses during the COVID-19 pandemic (BREATHE / EAVE II / National Core Studies) including analyses undertaken at the request of government and global health organisations; the use of analysis protocols and pooled analyses across several national TREs to demonstrate vaccine effectiveness in different groups; application of learning from this work to inform work on NHS Winter Pressures; analysis of respiratory-related hospital admissions; and the ongoing need for whole system intelligence. |
| Year(s) Of Engagement Activity | 2023 |
| Description | NIHR Respiratory Translational Research Collaboration: National Asthma Research Strategy Group meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The NIHR Respiratory Translational Research Collaboration (Respiratory TRC) brings together internationally recognised investigators in the UK's leading centres of excellence to carry out experimental and early phase research with industry, charities and other funders. Prof Jenni Quint spoke at the National Asthma Research Strategy Group meeting about "Digital and data / HDR UK workstream - where next?" |
| Year(s) Of Engagement Activity | 2023 |
| Description | Standing Committee on Pandemic Preparedness |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The Standing Committee on Pandemic Preparedness is a permanent advisory group to the Scottish Government, established to bring together scientists and technical experts to advise the Scottish Government on the future risks from pandemics and to ensure preparedness. The group makes recommendations to the First Minister and Scottish Cabinet. |
| Year(s) Of Engagement Activity | 2022,2023,2024 |
| URL | https://www.gov.scot/groups/standing-committee-on-pandemic-preparedness |
| Description | Webinar: Introducing Inflammation and Immunity |
| 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 | The webinar was to introduce the HDR UK Inflammation and Immunity Driver Programme to a wider audience; showcase the team's previous work in collaborative and standardised data curation for common respiratory conditions across the 4 UK nations (funded by BREATHE, MRC and Imperial BRC); and provide an opportunity for audience members to either ask questions about the programme, or about what to expect when engaging with our partnered data providers (CPRD, DataLoch, Honest Broker Service and SAIL Databank) |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.ed.ac.uk/usher/inflammation-and-immunity/events/introducing-inflammation-and-immunity |