Asthma

Eleanor L Axson, Jennifer K Quint

PH12 / 24 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    01/01/2001 - 31/12/2019
    Coding System
    SNOMED CT codesICD10 codesICD11 codesRead codes v2UKBioBank codes
    Data Sources
    UK Biobank , CPRD Aurum , Death Registration data for CPRD Aurum , CPRD GOLD , Death Registration data for CPRD GOLD , HES Admitted Patient Care data for CPRD Aurum , HES Admitted Patient Care data for CPRD GOLD
    Collections
    BREATHEPhenotype Library
    Tags
    No data

  2. Definition

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

    For those interested in further discrimination of asthma phenotypes, we refer you to Nissen et al. 2019.

    F. Nissen, Douglas, I. J., Mullerova, H., Pearce, N., Bloom, C. I., Smeeth, L., and Quint, J. K., ?Clinical profile of predefined asthma phenotypes in a large cohort of UK primary care patients (Clinical Practice Research Datalink)?, J Asthma Allergy, vol. 12, pp. 7-19, 2019.

    Validation of Read Codes for the Identification of COPD in CPRD

    Quint 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

    Phenoflow ID
    https://kclhi.org/phenoflow/phenotype/download/40

    Implementation

    No data

  4. Clinical Code List

  5. Publication

    • Publications from 2019 using validated Read codes from Nissen et al. 2017

    • F. Nissen, Douglas, I. J., Mullerova, H., Pearce, N., Bloom, C. I., Smeeth, L., and Quint, J. K., ?Clinical profile of predefined asthma phenotypes in a large cohort of UK primary care patients (Clinical Practice Research Datalink)?, J Asthma Allergy, vol. 12, pp. 7-19, 2019."

    • C. I. Bloom, Walker, S., and Quint, J. K., ?Inadequate specialist care referrals for high-risk asthma patients in the UK: an adult population-based cohort 2006-2017?, J Asthma, pp. 1-7, 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."

    • Publications from 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."

    • Wellcome Open Research

    • https://osf.io/kfz3n/

    Citation Requirements

    No data

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH12/version/24/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(
     'PH12',
     version_id=24
    )

    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(
     'PH12',
     version_id=24
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH12/version/24/export/codes/?format=json
    CSV site_root/phenotypes/PH12/version/24/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(
     'PH12',
     version_id=24
    )

    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(
     'PH12',
     version_id=24
    )

  7. Version History

    Version IDNameOwnerPublish date
    24 Asthma ieuan.scanlon2021-10-06currently shown