Atrial Fibrillation
Katherine I. Morley, Joshua Wallace , Spiros C. Denaxas, Ross J. Hunter, Riyaz S. Patel, Pablo Perel, Anoop D. Shah, Adam D. Timmis, Richard J. Schilling, Harry Hemingway
PH1025 / 2259 Clinical-Coded Phenotype
Overview
Phenotype TypeDisease or syndromePhenotype UUIDZFkKuf77cwvNohEH2vtit7SexBothValid Event Date Range01/01/1999 - 01/07/2016Coding SystemICD10 codesRead codes v2OPCS4 codesGPRD product codesData SourcesCollectionsCALIBERTagsNo dataDefinition
Combining evidence across sources to define and date phenotypes
The case definition for AF has three categories: * Historical: first recorded AF code indicates monitoring of an existing condition, or reference to a previous AF diagnosis. * Diagnosed: first record is a diagnosis code for AF; preference given to the earliest dated record rather than diagnosis source (i.e. no preference for primary versus secondary care). * Inferred: no diagnosis code is present, but the patient record includes a warfarin prescription in the absence of prior DVT or PE, or a digoxin prescription in the absence of HF. The phenotype algorithm incorporates these definitions in a hierarchical, mutually exclusive manner (see FIGURE). If the earliest recorded AF codes relate to a historical diagnosis or monitoring, the patient is in category 1 which precludes inclusion in other categories. If these codes are absent, then the presence of a coded diagnosis from primary or secondary care places a patient in category 2. Finally, in the absence of a coded diagnosis, a patient may be allocated to category 3, depending on the combination of prescriptions and diagnoses in their record. Otherwise a participant is treated as undiagnosed. ![Flow chart diagram illustrating the CALIBER phenotype algorithm for atrial fibrillation][images/af_flowchart.jpeg]
Implementation
Implementation
Clinical Code List
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Publication
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Pasea L et al. Personalising the decision for prolonged dual antiplatelet therapy: development, validation and potential impact of prognostic models for cardiovascular events and bleeding in myocardial infarction survivors. Eur Heart J. 2017 Apr 7;38(14):1048-1055. doi: 10.1093/eurheartj/ehw683. PMID: 28329300
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(DOI:10.1136/heartjnl-2015-308850)Daskalopoulou M et al. Depression as a Risk Factor for the Initial Presentation of Twelve Cardiac, Cerebrovascular, and Peripheral Arterial Diseases: Data Linkage Study of 1.9 Million Women and Men. PLoS One. 2016 Apr 22;11(4):e0153838. doi: 10.1371/journal.pone.0153838. eCollection 2016. PMID: 27105076
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(DOI:10.1136/heartjnl-2015-308514)Pujades-Rodriguez M et al. Rheumatoid Arthritis and Incidence of Twelve Initial Presentations of Cardiovascular Disease: A Population Record-Linkage Cohort Study in England. PLoS One. 2016 Mar 15;11(3):e0151245. doi: 10.1371/journal.pone.0151245. eCollection 2016. PMID: 26978266
(DOI:10.1371/journal.pone.0151245)Shah AD et al. Low eosinophil and low lymphocyte counts and the incidence of 12 cardiovascular diseases: a CALIBER cohort study. Open Heart. 2016 Sep 5;3(2):e000477. doi: 10.1136/openhrt-2016-000477. eCollection 2016. PMID: 27621833
(DOI:10.1136/openhrt-2016-000477)Timmis A et al. Prolonged dual antiplatelet therapy in stable coronary disease: comparative observational study of benefits and harms in unselected versus trial populations. BMJ. 2016 Jun 22;353:i3163. PMID: 27334486
Walker S et al. Long-term healthcare use and costs in patients with stable coronary artery disease: a population-based cohort using linked health records (CALIBER). Eur Heart J Qual Care Clin Outcomes. 2016 Jan 20;2(2):125-140. doi: 10.1093/ehjqcco/qcw003. PMID: 27042338
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(DOI:10.1161/CIRCULATIONAHA.114.013797)Morley KI et al. Defining disease phenotypes using national linked electronic health records: a case study of atrial fibrillation. PLoS One. 2014 Nov 4;9(11):e110900. doi: 10.1371/journal.pone.0110900. eCollection 2014. PMID: 25369203
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(DOI:10.1093/eurheartj/eht533)
Citation Example
Katherine I. Morley, Joshua Wallace , Spiros C. Denaxas, Ross J. Hunter, Riyaz S. Patel, Pablo Perel, Anoop D. Shah, Adam D. Timmis, Richard J. Schilling, Harry Hemingway. PH1025 / 2259 - Atrial Fibrillation. Phenotype Library [Online]. 23 August 2022. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH1025/version/2259/detail/. [Accessed 08 September 2024]
API
To Export Phenotype Details:
Format API JSON site_root/api/v1/phenotypes/PH1025/version/2259/detail/?format=json R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get details of phenotype
phenotype_details = client$phenotypes$get_detail(
'PH1025',
version_id=2259
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_detail(
'PH1025',
version_id=2259
)To Export Phenotype Code List:
Format API JSON site_root/api/v1/phenotypes/PH1025/version/2259/export/codes/?format=json CSV site_root/phenotypes/PH1025/version/2259/export/codes/ R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get codelist of phenotype
phenotype_codelist = client$phenotypes$get_codelist(
'PH1025',
version_id=2259
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_codelist(
'PH1025',
version_id=2259
)Version History