Chronic obstructive pulmonary disease (COPD) Biobank

Eleanor L Axson, Jennifer K Quint, Mome Mukherjee, Hannah R Whittaker, Philip W Stone, Kate McLaren

PH799 / 2223 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    01/01/2020 to 31/01/2021
    Coding System
    UKBioBank codes
    Data Sources
    UK Biobank
    Collections
    BREATHEPhenotype Library
    Tags
    No data

  2. Definition

    • copd
    • Validation of Read Codes for the Identification of COPD in CPRDQuint et al. validated a set of Read codes for the identification of COPD in CPRD in 2014. Using diagnostic codes alone, the positive predictive value (PPV) was 86.5% (77.5–92.3%). Requiring a diagnostic code, spirometry measures, and specific medication increased PPV to 89.4% (80.7–94.5%) but reduced case numbers by 10%.

  3. Implementation

    Implementation

    These codes are not intended to be mandatory, but are to be used as a starting point for the identification of COPD in routine EHR. Each study may differ in the sensitivity and specificity of the coding required.

    According to the National Institute for Health and Care Excellence (NICE) guidelines for the diagnosis of COPD, COPD should be suspected in patients over 35 years old who have a risk factor (typically smoking) and at least one symptom. It is therefore recommended that these codes are only utilised in an adult population at least 35 years old with a history of smoking.

    https://www.nice.org.uk/guidance/ng115/chapter/Recommendations#diagnosing-copd

    Use the following terms to find COPD codes in code browsers

    Note: * is a wildcard indicating inclusion of any characters

    Search terms:

    *copd*

    *chronic obstructive pulmonary disease*

    *emphysema*

    *airway obstruction*

    *airway obstrucn*

    *emphysematous*

    *chronic obstructive airways*

    *chronic obstructive*

    Exclude terms:

    "subcutaneous emphysema"

  4. Clinical Code List

  5. Publication

    • Publications in 2019 using validated Read codes from Quint et al. 2014

    • D. Stolz, Kostikas, K., Loefroth, E., Fogel, R., Gutzwiller, F. S., Conti, V., Cao, H., and Clemens, A., “Differences in COPD exacerbation risk between women and men: analysis from the UK Clinical Practice Research Datalink data”, Chest, 2019.

    • M. Pikoula, Quint, J. K., Nissen, F., Hemingway, H., Smeeth, L., and Denaxas, S., “Identifying clinically important COPD sub-types using data-driven approaches in primary care population based electronic health records”, BMC Med Inform Decis Mak, vol. 19, p. 86, 2019.

    • H. R. Whittaker, Mullerova, H., Jarvis, D., Barnes, N. C., Jones, P. W., Compton, C. H., Kiddle, S. J., and Quint, J. K., “Inhaled corticosteroids, blood eosinophils, and FEV1 decline in patients with COPD in a large UK primary health care setting”, Int J Chron Obstruct Pulmon Dis, vol. 14, pp. 1063-1073, 2019.

    • C. I. Bloom, Ricciardi, F., Smeeth, L., Stone, P., and Quint, J. K., “Predicting COPD 1-year mortality using prognostic predictors routinely measured in primary care”, BMC Med, vol. 17, p. 73, 2019.

    • D. Dedman, Coton, S. J., Ghosh, R. E., Meeraus, W., Crim, C., Harvey, C., Amelio, J., and Landis, S. H., “Treatment Patterns of New Users of Fluticasone Furoate/Vilanterol in Asthma and COPD in UK Primary Care: Retrospective Cohort Study”, Pulmonary Therapy, vol. 5, pp. 81-95, 2019.

    • J. D. Chalmers, Poole, C., Webster, S., Tebboth, A., Dickinson, S., and Gayle, A., “Assessing the healthcare resource use associated with inappropriate prescribing of inhaled corticosteroids for people with chronic obstructive pulmonary disease (COPD) in GOLD groups A or B: an observational study using the Clinical Practice Research Data”, Respir Res, vol. 19, p. 63, 2018.

    • Publications in 2019 using Read codes from QOF

    • P. Rockenschaub, Jhass, A., Freemantle, N., Aryee, A., Rafiq, M., Hayward, A., and Shallcross, L., “Opportunities to reduce antibiotic prescribing for patients with COPD in primary care: a cohort study using electronic health records from the Clinical Practice Research Datalink (CPRD)”, J Antimicrob Chemother, 2019.

    • Publications in 2020

    • Found articles with screening decisions can be found at:

    • https://www.zotero.org/groups/2751849/copd_search_for_codes/library

    • Publications in 2020 using validated Read codes from Quint et al. 2014

    • Axson et al. "Temporal Trends in the Incidence of Heart Failure among Patients with Chronic Obstructive Pulmonary Disease and Its Association with Mortality." 10.1513/AnnalsATS.201911-820OC

      (DOI:10.1513/AnnalsATS.201911-820OC)

    • Bloom et al. "Inhaled Corticosteroid Treatment Regimens and Health Outcomes in a UK COPD Population Study." 10.2147/COPD.S241568

      (DOI:10.2147/COPD.S241568)

    • Kiddle et al. "Prediction of five-year mortality after COPD diagnosis using primary care records." 10.1371/journal.pone.0236011

      (DOI:10.1371/journal.pone.0236011)

    • Kositkas et al. "Clinical Impact and Healthcare Resource Utilization Associated with Early versus Late COPD Diagnosis in Patients from UK CPRD Database." 10.2147/COPD.S255414

      (DOI:10.2147/COPD.S255414)

    • Requena et al. "Feasibility of using Clinical Practice Research Datalink data to identify patients with chronic obstructive pulmonary disease to enrol into real-world trials." 10.1002/pds.5188

      (DOI:10.1002/pds.5188)

    • Schultze et al. "Risk of COVID-19-related death among patients with chronic obstructive pulmonary disease or asthma prescribed inhaled corticosteroids: an observational cohort study using the OpenSAFELY platform." 10.1016/S2213-2600(20)30415-X

      (DOI:10.1016/S2213-2600(20)30415-X)

    • Stone et al. "Predictors of Referral to Pulmonary Rehabilitation from UK Primary Care."10.2147/COPD.S273336

      (DOI:10.2147/COPD.S273336)

    • Whittaker et al. "Accelerated FEV1 decline and risk of cardiovascular disease and mortality in a primary care population of COPD patients." 10.1183/13993003.00918-2020

      (DOI:10.1183/13993003.00918-2020)

    • Whittaker et al. "Eligibility for Lung Volume Reduction Surgery in Patients With COPD Identified in a UK Primary Care Setting."10.1016/j.chest.2019.07.016

      (DOI:10.1016/j.chest.2019.07.016)

    • Whittaker et al. "Characteristics Associated with Accelerated Lung Function Decline in a Primary Care Population with Chronic Obstructive Pulmonary Disease."10.2147/COPD.S278981

      (DOI:10.2147/COPD.S278981)

    • Publications in 2020 using Read codes from QOF

    • Kerkhof et al. "Association between COPD exacerbations and lung function decline during maintenance therapy." 10.1136/thoraxjnl-2019-214457

      (DOI:10.1136/thoraxjnl-2019-214457)

    • Mehta et al. "COPD and asthma in patients with opioid dependency: a cross-sectional study in primary care."10.1038/s41533-019-0161-7

      (DOI:10.1038/s41533-019-0161-7)

    • Rockenschaub et al. "Antibiotic Prescribing Before and After the Diagnosis of Comorbidity: A Cohort Study Using Primary Care Electronic Health Records." 10.1093/cid/ciz1016

      (DOI:10.1093/cid/ciz1016)

    • Rockenschaub et al. "Antibiotic Prescribing Before and After the Diagnosis of Comorbidity: A Cohort Study Using Primary Care Electronic Health Records."10.1093/jac/dkz411

      (DOI:10.1093/jac/dkz411)

    • Publications in 2020 using Read codes from TargetCOPD (Jordan et al. 2016)

    • Dickens et al. "Accuracy of Vitalograph lung monitor as a screening test for COPD in primary care."10.1038/s41533-019-0158-2

      (DOI:10.1038/s41533-019-0158-2)

    • Haroon et al. "Impact of COPD case finding on clinical care: a prospective analysis of the TargetCOPD trial."10.1136/bmjopen-2020-038286

      (DOI:10.1136/bmjopen-2020-038286)

    • Publications in 2020 using ICD-9/ICD-10 codes from Gershon et al. 2009

    • Baliunas et al. "Variability in patient sociodemographics, clinical characteristics, and healthcare service utilization among 107,302 treatment seeking smokers in Ontario: A cross-sectional comparison." 10.1371/journal.pone.0235709

      (DOI:10.1371/journal.pone.0235709)

    • Johnson et al. "Healthcare system encounters before COPD diagnosis: a registry-based longitudinal cohort study." 10.1136/thoraxjnl-2019-213554

      (DOI:10.1136/thoraxjnl-2019-213554)

    • Code repositories

    • ID- Cambridge COP087 - Repository- University of Cambridge Primary Care Unit - Description- CPRD @ Cambridge – [v1.0 ARCHIVED] – August 2017 (GOLD): COPD codelist: CPRD Cambridge created, based on the QOF2012 list. Likely to be sensitive as broad range of codes. (CPRDCAM_COP087_MEDCODES) - Publication- QOF 2012

    • ID- Cambridge COP151 - Repository- University of Cambridge Primary Care Unit - Description- CPRD @ Cambridge – Codes Lists (GOLD): COPD: List developed by Cambridge CPRD group, based on the QOF2012 list. Likely to be sensitive as broad range of codes. (COP151) - Publication- QOF 2012

    • ID- Cambridge COPD_COD - Repository- University of Cambridge Primary Care Unit - Description- CPRD @ Cambridge – Code Lists (QOFv44 Business Rules): QOF SNOMED -> CPRD Aurum (COPD: COPD_COD) - Publication- https://digital.nhs.uk/data-and-information/data-collections-and-data-sets/data-collections/quality-and-outcomes-framework-qof/quality-and-outcome-framework-qof-business-rules/quality-and-outcomes-framework-qof-business-rules-v44-2019-2020-october-2020-release

    • ID- LSHTM Data Compass 340 - Repository- LSHTM Data Compass - Description- Clinical code list - COPD codes - Publication-

    • ID- LSHTM Data Compass 859 - Repository- LSHTM Data Compass - Description- Clinical Codelist - Read codes for COPD - Publication-

    • ID- LSHTM Data Compass 1134 - Repository- LSHTM Data Compass - Description- Covariate Code List - COPD - Publication-

    • ID- LSHTM Data Compass 1600 - Repository- LSHTM Data Compass - Description- Clinical Code List - Zoster Comorbidity Read Codes - Publication-

    • ID- LSHTM Data Compass 1601 - Repository- LSHTM Data Compass - Description- Clinical Code List - Zoster Comorbidity Read Codes - Publication-

    • ID- LSHTM Data Compass 1682 - Repository- LSHTM Data Compass - Description- Clinical codelist - Chronic pulmonary disease codes - Publication-

    • ID- LSHTM Data Compass 2036 - Repository- LSHTM Data Compass - Description- Clinical codelist - Chronic Obstructive Pulmonary Disease read codes - Publication-

    • ID- LSHTM Data Compass 2037 - Repository- LSHTM Data Compass - Description- Clinical codelist - Chronic Obstructive Pulmonary Disease ICD-10 codes - Publication-

    • ID- Manchester Clinical Codes 1 - Repository- Manchester Clinical Codes - Description- QOF Business Rules v24 - Publication- QOF v24

    • ID- Manchester Clinical Codes 2 - Repository- Manchester Clinical Codes - Description- QOF Business Rules v5 - Publication- QOF v5

    • ID- Manchester Clinical Codes 5 - Repository- Manchester Clinical Codes - Description- Withdrawing Performance Indicators: Retrospective Analysis of General Practice Performance Under the UKs Quality and Outcomes Framework - Publication- https://doi.org/10.1136/bmj.g330

      (DOI:10.1136/bmj.g330)

    • ID- Manchester Clinical Codes 6 - Repository- Manchester Clinical Codes - Description- Effect of financial incentives on incentivised and non-incentivised clinical activities: longitudinal analysis of data from the UK Quality and Outcomes Framework - Publication- https://doi.org/10.1136/bmj.d3590

      (DOI:10.1136/bmj.d3590)

    • ID- Manchester Clinical Codes 9 - Repository- Manchester Clinical Codes - Description- Glucose, blood pressure and cholesterol levels and their relationships to clinical outcomes in type 2 diabetes: a retrospective cohort study - Publication- https://doi.org/10.1007/s00125-014-3473-8

      (DOI:10.1007/s00125-014-3473-8)

    • ID- Manchester Clinical Codes 21 - Repository- Manchester Clinical Codes - Description- Primary care consultation rates among people with and without severe mental illness: a UK cohort study using the Clinical Practice Research Datalink - Publication- http://dx.doi.org/10.1136/bmjopen-2015-008650

      (DOI:10.1136/bmjopen-2015-008650)

    • ID- Manchester Clinical Codes 26 - Repository- Manchester Clinical Codes - Description- Inequalities in physical co-morbidity: A longitudinal comparative observational study of people with severe mental illness in the UK - Publication- http://dx.doi.org/10.1136/bmjopen-2015-009010

      (DOI:10.1136/bmjopen-2015-009010)

    • ID- Manchester Clinical Codes 43 - Repository- Manchester Clinical Codes - Description- Recorded quality of primary care for patients with diabetes in England before and after the introduction of a financial incentive scheme: a longitudinal observational study - Publication- http://dx.doi.org/10.1136/bmjqs-2012-001033

      (DOI:10.1136/bmjqs-2012-001033)

    • ID- - Repository- OpenSAFELY Codelists - Description- Current COPD: Codelist indicating current COPD. - Publication-

    Citation Example

    Eleanor L Axson, Jennifer K Quint, Mome Mukherjee, Hannah R Whittaker, Philip W Stone, Kate McLaren. PH799 / 2223 - Chronic obstructive pulmonary disease (COPD) Biobank. Phenotype Library [Online]. 04 August 2022. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH799/version/2223/detail/. [Accessed 31 October 2024]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH799/version/2223/detail/?format=json
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get details of phenotype

    phenotype_details = client$phenotypes$get_detail(
     'PH799',
     version_id=2223
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of phenotype

    phenotype_codelist = client.phenotypes.get_detail(
     'PH799',
     version_id=2223
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH799/version/2223/export/codes/?format=json
    CSV site_root/phenotypes/PH799/version/2223/export/codes/
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get codelist of phenotype

    phenotype_codelist = client$phenotypes$get_codelist(
     'PH799',
     version_id=2223
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of phenotype

    phenotype_codelist = client.phenotypes.get_codelist(
     'PH799',
     version_id=2223
    )

  7. Version History

    Version IDNameOwnerPublish date
    2223 Chronic obstructive pulmonary disease (COPD) Biobank zinnurar2022-08-08currently shown
    1677 Chronic obstructive pulmonary disease (COPD) Biobank zinnurar2022-01-17