Recent publications from research developed in EPCC’s Safe Haven
25 April 2024
Two key papers on COVID outcomes have been published recently, both of which used the Outbreak Data Analysis Platform (ODAP) hosted and managed by EPCC’s Safe Haven Services. One paper looks at indicators for long COVID and the other at outcomes for cancer patients with COVID.
The Outbreak Data Analysis Platform (ODAP) was developed in 2020 to house research data for the ISARIC-4C COVID-19 study and to link this to NHS and other research data such as PHOSP-COVID (Post Hospitalisation COVID-19) in a secure environment for analysis.
ODAP is a collaborative programme between the ISARIC-4C team (headed by CI Prof. Callum Semple at the University of Liverpool and co-investigator Prof. Kenneth Baillie at the University of Edinburgh), Public Health Scotland’s Electronic Data Research and Innovation Service (eDRIS) who run the Scottish National Safe Haven (SNSH), and EPCC.
ISARIC-4C collected data on over 300,000 COVID hospitalised patients in the UK at different timepoints, including a range of information on symptoms, test results, and intensive care treatment. The PHOSP-COVID study collected follow-up data on some of these patients after their discharge from hospital.
The study data used in this research, along with NHS data from England and Scotland, was held in the SNSH, which EPCC operates on behalf of eDRIS. EPCC additionally provided data engineering skills: under instruction from eDRIS and the ISARIC-4C team, we removed personal identifiers and curated, catalogued and linked the data, creating extracts for researchers. As with all projects in the SNSH, each study first went through a strict application process before gaining access to particular subsets of the data relevant to its research.
EPCC then provided data extracts to researchers via eDRIS in their own study area of the SNSH where they could analyse data in a secure, isolated environment. Only approved researchers who have completed the relevant training are allowed to use the Safe Haven. On completion of analysis, outputs for publication which summarise findings were extracted from the Safe Haven by eDRIS, following Statistical Disclosure Checks to ensure that no data relating to individual people was included.
Large-scale phenotyping
Of the recent publications, the first was in Nature and led by Felicity Liew of Imperial College, London. Using PHOSP-COVID data, this study looked at large-scale phenotyping of patients with long COVID post-hospitalisation and showed evidence of ongoing inflammation in the blood. These findings could help to inform further understanding and research into the condition.
Changes in hospital mortality in patients with cancer
The second study, published in Lancet Oncology, was led by Prof. Lance Turtle of the University of Liverpool. Using ISARIC-4C data, this looked at changes in hospital mortality in patients with cancer during the pandemic. It showed that people with cancer have a higher risk of mortality from COVID-19 than those without cancer.
EPCC Trusted Research Environment
A Trusted Research Environment is a highly secure data and compute infrastructure where de-identified sensitive data is made available for analysis. EPCC operates a Trusted Research Environment to host Safe Haven Services owned and controlled by other organisations.
In this environment organisations can create and control their own Safe Haven Services to provide access to unconsented NHS data (see: https://www.epcc.ed.ac.uk/whats-happening/articles/national-safe-haven-research-using-unconsented-nhs-data). Each Safe Haven is isolated from all other Safe Havens, and a Safe Haven owner can run independent projects where they control who has access to which projects.
Safe Havens hosted in the EPCC Trusted Research Environment include the Scottish National Safe Haven, a governed trusted research environment for accredited researchers to work on approved projects of public benefit using sensitive data. Among our other tenants are Smart Data Foundry (financial data); DataLoch (health and social care data), and Childlight (data related to child protection).
Further information
Changes in hospital mortality in patients with cancer during the COVID-19 pandemic (ISARIC-CCP-UK): a prospective, multicentre cohort study: https://www.thelancet.com/journals/lanonc/article/PIIS1470-2045%2824%2900107-4/fulltext#seccestitle10
Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease: https://www.nature.com/articles/s41590-024-01778-0
ISARIC-4C: https://isaric4c.net
ODAP: https://odap.ac.uk
PHOSP-COVID: https://www.phosp.org
Safe Haven Services: https://edinburgh-international-data-facility.ed.ac.uk/services/safe-haven-services
To discuss access to our Safe Haven Services, please contact us at: eidf@epcc.ed.ac.uk