Inflammation and Immunity
Lead Research Organisation:
Health Data Research UK
Department Name: UNLISTED
Abstract
The Inflammation and Immunity research programme will transform the UK capabilities to understand the inner workings of disease. The research will develop ways to map the people suffering from common allergic and breathing conditions alongside information on their care and outcomes across the UK. The maps will be used to explore variation in how people are cared for and develop tools to help healthcare services improve and reduce inequalities.
This will lay the foundations, building tools and new ways, for other researchers to understand and improve care for other causes of breathing conditions, and develop ways to better predict, prevent and manage illness.
This will lay the foundations, building tools and new ways, for other researchers to understand and improve care for other causes of breathing conditions, and develop ways to better predict, prevent and manage illness.
Technical Summary
This work is funded by the UKRI Medical Research Council, UKRI Engineering and Physical Sciences Research Council, UKRI Economic and Social Research Council, Department of Health and Social Care, National Institute for Health Research (England), Chief Scientist Office (Scottish Government), Health and Care Research Wales, Public Health Agency HSC (Northern Ireland), British Heart Foundation and Cancer Research UK
The Inflammation and Immunity Driver Programme will explore inflammation and immunity as general underpinning mechanisms, using highly prevalent respiratory and allergic diseases in the first instance. These illnesses can be exacerbated by acute inflammatory episodes due to infections (i.e., rhinovirus, coronaviruses, influenza, pneumonia, RSV), pollution, tobacco, pollen, weather, drugs, foods and stinging insects, and are exemplars of seasonal, chronic inflammatory respiratory illnesses. Although efforts will initially be focused here, the long-term plan is to extend the data science capabilities and capacity to other inflammatory mediated diseases in the future.
Impact and legacy
The programme will provide a data foundation to contribute to novel respiratory health and clinical strategies that better predict, prevent and manage respiratory conditions. The programme will follow the principles of team science and build on the achievements of the first five years made by the team and by HDR UK more widely. This will include building on and developing new collaborations developed through the BREATHE Hub and leveraging core support by attracting external funding. It will give back to the scientific community by developing open-source tools and methods, providing a framework and approach for studying the surveillance and trajectory of other inflammatory and immune disorders. The programme will develop future research leaders and engage with and involve patients and the public through all workstreams whilst contributing to and utilising the HDR UK Infrastructure and Services pillars and global strategy.
The Inflammation and Immunity Driver Programme will explore inflammation and immunity as general underpinning mechanisms, using highly prevalent respiratory and allergic diseases in the first instance. These illnesses can be exacerbated by acute inflammatory episodes due to infections (i.e., rhinovirus, coronaviruses, influenza, pneumonia, RSV), pollution, tobacco, pollen, weather, drugs, foods and stinging insects, and are exemplars of seasonal, chronic inflammatory respiratory illnesses. Although efforts will initially be focused here, the long-term plan is to extend the data science capabilities and capacity to other inflammatory mediated diseases in the future.
Impact and legacy
The programme will provide a data foundation to contribute to novel respiratory health and clinical strategies that better predict, prevent and manage respiratory conditions. The programme will follow the principles of team science and build on the achievements of the first five years made by the team and by HDR UK more widely. This will include building on and developing new collaborations developed through the BREATHE Hub and leveraging core support by attracting external funding. It will give back to the scientific community by developing open-source tools and methods, providing a framework and approach for studying the surveillance and trajectory of other inflammatory and immune disorders. The programme will develop future research leaders and engage with and involve patients and the public through all workstreams whilst contributing to and utilising the HDR UK Infrastructure and Services pillars and global strategy.
Organisations
- Health Data Research UK (Lead Research Organisation)
- UNIVERSITY OF OXFORD (Collaboration)
- Meteorological Office UK (Collaboration)
- SAIL Databank (Collaboration)
- London School of Hygiene and Tropical Medicine (LSHTM) (Collaboration)
- Asthma + Lung UK (Collaboration)
- Medicines and Healthcare Regulatory Agency (Collaboration)
- HEALTH DATA RESEARCH UK (Collaboration)
- Royal College of Physicians of London (Collaboration)
- QUEEN'S UNIVERSITY BELFAST (Collaboration)
| Description | CMO meeting: update on EAVE II and future plans |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Contribution to Medical Schools Council |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Global Initiative for Asthma (GINA) - Scientific Committee |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Contributions to messaging for GINA 2024 report, clinical advice for diagnosis of asthma, management of exacerbations in primary care, ongoing discussions around changes in management of asthma in children 6-12 years and allergen immunotherapy. |
| Description | Scottish Government Public Health Advisory Forum |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Commercial funding |
| Amount | $385,000 (USD) |
| Organisation | Insmed |
| Sector | Private |
| Country | United States |
| Start | 03/2024 |
| End | 10/2025 |
| Description | Enhancing public health readiness and response |
| Amount | £35,000 (GBP) |
| Organisation | UK Health Security Agency |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2024 |
| End | 06/2024 |
| Description | National Respiratory Audit Programme |
| Amount | £59,682 (GBP) |
| Organisation | Royal College of Physicians of London |
| Sector | Learned Society |
| Country | United Kingdom |
| Start | 09/2023 |
| End | 03/2027 |
| Description | Precision Medicine Doctoral Training Programme |
| Amount | £96,688 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2024 |
| End | 02/2028 |
| Description | Respiratory Data Science Catalyst |
| Amount | £500,000 (GBP) |
| Organisation | Asthma + Lung UK |
| Sector | Charity/Non Profit |
| 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 | A+LUK |
| Organisation | Asthma + Lung UK |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Discussions in 2022: information about the potential use of EHRs and the potential of wider data linkage to address key policy questions around incidence, prevalence and health economics of respiratory diseases. |
| Collaborator Contribution | Partnership agreed in 2023 with HDR UK. Includes £500,000 in funding for a data science catalyst in respiratory medicine |
| Impact | HDR UK is seeking to second an Associate Director to take on leadership of a new data science catalyst in respiratory medicine. |
| Start Year | 2022 |
| Description | BHF Data Science Centre |
| Organisation | Health Data Research UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Prof Jenni Quint led discussions with the British Heart Foundation Data Science Centre (BHF DSC) to utilise their data infrastructure to answer questions about comorbidities between CVD and lung disease. |
| Collaborator Contribution | The HDR UK BHF DSC team provided support to the BREATHE analysts to explore opportunities and address data queries. |
| Impact | Findings contributed to our understanding of complications following COVID-19 in people with lung disease. |
| Start Year | 2022 |
| Description | CPRD & SAIL Databank |
| Organisation | Medicines and Healthcare Regulatory Agency |
| Department | Clinical Practice Research Datalink (CPRD) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Curation of code for asthma, COPD and ILD in primary and linked secondary care data in England and Wales. |
| Collaborator Contribution | Provision of anonymised patient data and governance oversight / management. |
| Impact | Project commissioned in 2022. COPD and ILD algorithms and code are to be made available as a research-ready resource and an improvement in data for industry, charity, academic and NHS use. Current status: the work is complete and a publication is in press (Feb 2024). Methods have been added to github and are listed in ResearchFish reports. This work has provides foundations for the HDR UK Inflammation and Immunity Driver Programme and work is continuing from this. |
| Start Year | 2021 |
| 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 | Immune Mediated Inflammatory Disease (IMID) |
| Organisation | London School of Hygiene and Tropical Medicine (LSHTM) |
| Department | Faculty of Epidemiology and Population Health |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Discussions with Inflammation and Immunity Driver Programme team. Contributions to a workshop in January 2024 |
| Collaborator Contribution | Convened a workshop with HDR UK and its driver programmes, to discuss research opportunities in relation to the common pathophysiological and therapeutic characteristics of IMIDs. A collaborative group has been formed to move away from siloed care and research, in particular to identify priorities for data access and linkage for transformative research. |
| Impact | A report has been circulated to collaborators from the workshop held in January 2024. |
| Start Year | 2023 |
| 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 | National Respiratory Audit Programme |
| Organisation | Royal College of Physicians of London |
| Department | National Chronic Obstructive Pulmonary Disease (COPD) Audit Programme |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Prof Jenni Quint contributes clinical and methodological expertise to the audit programme. |
| Collaborator Contribution | NRAP has contributed half the costs of a PhD at Imperial to the Inflammation and Immunity Driver Programme |
| Impact | Harley Kwok's PhD begain in October 2023. This is exploring COPD phenotypes, treatments and progression. |
| Start Year | 2023 |
| Description | Pathogen X / UKHSA |
| Organisation | University of Oxford |
| Department | Nuffield Department of Primary Care Health Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collaboration between University of Edinburgh, EAVE II collaborators and University of Oxford to develop a set of well-defined analysis plans that build on associated, field tested, protocols and analysis plans for rapid assessment of pathogen transmission and vaccine and therapeutic effectiveness and safety for potential future respiratory pathogens. We have developed a project analysis plan and described the data to be used to provide insights for future pathogen modelling work. Protocols are in development, adapted from the EAVE II statistical analysis plans and GitHub repository. |
| Collaborator Contribution | Work has only recently started / is ongoing, but builds on previous COVID-19 collaborations funded through MRC, National Core Studies and HDR UK. The University of Oxford is the home of the primary care sentinel network (the Royal College of General Practitioners Research and Surveillance Centre (RCGP RSC)), and is a primary source for disease surveillance in England (around 2000 general practices) and virological sampling data. The RCGP RSC works closely with the UK Health Security Agency to monitor infectious diseases with a focus on respiratory viruses. The RCGP RSC provides vaccine effectiveness estimates and characterises vulnerable populations. |
| Impact | The collaboration began in December 2023, so it is too early to list outputs or outcomes. |
| Start Year | 2023 |
| 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 |