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Longitudinal C-reactive protein concentrations in COVID-19: an OMOP dataset

Dataset
Version: 1.0.0
CRP has been identified as a biomarker of importance in COVID. This OMOP dataset features highly granular health data from over 4500 patients with hospitalised COVID-19, including oxygen support and treatments given.

Summary

Citation:
Longitudinal C-reactive protein concentrations in COVID-19: an OMOP dataset

Documentation

Description:
C-reactive protein (CRP) is the classical acute-phase protein produced by the liver at rates regulated by pro-inflammatory cytokines, notably IL-6. Acute phase CRP production is non-specific but generally reflects the extent and severity of whatever infective, inflammatory, traumatic and neoplastic conditions have triggered it (Pepys, M. B. & Hirschfield, G. M. J. Clin. Invest. 111, 1805-1812 (2003). CRP binds specifically to dead or dying cells and then activates complement, leading to enhanced inflammation and exacerbation of pre-existing tissue damage (Griselli, M. et al. J. Exp. Med. 190, 1733-1739 (1999). Large amounts of CRP in the blood can also increase damage to tissues that are already injured. CRP may thus contribute to disease severity and death in COVID-19. Circulating CRP values in COVID-19 patients are closely associated with disease activity, severity and outcome (for example: L. Yan et al. (2020) https://doi.org/10.1038/s42256-020-0180-7 ). However, the published studies are of moderate size with only one or few CRP measurements per patient. In this OMOP dataset, we present longitudinal CRP measurements for a cohort of over 4500 hospitalised COVID-19 patients, from admission to discharge, including severity of disease, co-morbidities, treatments given, complications, ITU admissions and patient outcomes. PIONEER geography: The West Midlands (WM) has a population of 5.9 million & includes a diverse ethnic & socio-economic mix. EHR. UHB is one of the largest NHS Trusts in England, providing direct acute services & specialist care across four hospital sites, with 2.2 million patient episodes per year, 2750 beds & an expanded 250 ITU bed capacity during COVID. UHB runs a fully electronic healthcare record (EHR) (PICS; Birmingham Systems), a shared primary & secondary care record (Your Care Connected) & a patient portal “My Health”. Scope: All hospitalised patients admitted to Queen Elizabeth Hospital, Birmingham with positive SARS-Cov2 tests reported, transformed into an extended set of tables based on OMOP. The dataset includes highly granular patient demographics & co-morbidities taken from ICD-10 & SNOMED-CT codes. Serial, structured data pertaining to process of care including timings, admissions, escalation of care to ITU, discharge outcomes, physiology readings (heart rate, blood pressure, AVPU score and others), blood results (especially C-Reactive Protein (CRP) measurements) and drug prescribing and administration data. Available supplementary data: Matched controls; ambulance, synthetic data. Available supplementary support: Analytics, Model build, validation & refinement; A.I.; Data partner support for ETL (extract, transform & load) process, Clinical expertise, Patient & end-user access, Purchaser access, Regulatory requirements, Data-driven trials, “fast screen” services.
Is Part Of:
NOT APPLICABLE

Coverage

Spatial:
United Kingdom, England, West Midlands
Typical Age Range:
18-105
Follow Up:
OTHER
Physical Sample Availability:
NOT AVAILABLE
Pathway:
Data is representative of the multi-ethnicity population within the West Midlands (42% non white). Data includes all patients admitted during this timeframe, with National data Opt Outs applied, and therefore is representative of admissions to secondary care. Data focuses on in-patient stay in hospital during the acute episode but can be supplemented on request to include previous and subsequent hospital contacts (including outpatient appointments) and ambulance, 111, 999 data.

Provenance

Origin

Purposes:
CARE
Sources:
EPR
Collection Situations:
IN-PATIENTS

Temporal

Accrual Periodicity:
QUARTERLY
Distribution Release Date:
2021-12-09
Start Date:
2019-12-23
End Date:
2021-07-29
Time Lag:
OTHER

Accessibility

Access

Access Service:
Trusted Research Environments (TRE) are built using Microsoft Azure services and hosted in the UK to provide research teams a safe, secure and agile environment which allows users to quickly analyse, interpret and form an enriched view of primary care information through a range of integrated datasets. Health data collated from multiple sources is ingested into a secure data lake which will then allow subsets of data to be made available to research teams on approval of a data request. Once approved a customer specific TRE is made available with a standard set of leading analytical tools from Microsoft including Azure Databricks, Azure Machine Learning, Azure SQL and Azure Synapse (for large-scale data warehouses). Specific tools can be provided at an additional cost over the standard platform data access charge and the PIONEER team will work with you to determine your exact needs. Access to the TRE is managed using the latest virtual desktop technology to provide a safe and secure end-user experience. By utilising leading edge design PIONEER are able to create TREs rapidly to enable us to service any customer requirement.
Access Request Cost:
www.pioneerdatahub.co.uk/data/data-services-costs/
Delivery Lead Time:
1-2 MONTHS
Jurisdictions:
GB-ENG
Data Controller:
University Hospitals Birmingham NHS Foundation Trust
Data Processor:
NOT APPLICABLE

Usage

Data Use Limitations:
GENERAL RESEARCH USE
Data Use Requirements:
PROJECT SPECIFIC RESTRICTIONS
Resource Creators:
  • This publication uses data from PIONEER
  • an ethically approved database and analytical environment (East Midlands Derby Research Ethics 20/EM/0158)

Format and Standards

Vocabulary Encoding Schemes:
SNOMED CT
Conforms To:
OMOP
Languages:
en
Formats:
SQL

Enrichment and Linkage

Derivations:
Not Available

Observations

Statistical Population
Population Description
Population Size
Measured Property
Observation Date
Events
4,790 distinct patients with CRP COVID visits between 23/12/2019 and 29/07/2021
4790
COUNT
2021-12-09