White Blood Cells
Shah A
PH353 / 706 Clinical-Coded Phenotype
Overview
Phenotype TypeBiomarkerPhenotype UUIDm9LJwQVE3LVudvQ5bCu6MZSexBothValid Event Date Range01/01/1999 - 01/07/2016Coding SystemRead codes v2Data SourcesCollectionsPhenotype LibraryTagsNo dataDefinition
Total white cell counts can be affected by many factors such as infections, autoimmune diseases, medication and haematological conditions. Similar to our recent study on eosinophil counts,1 we sought to differentiate between a patient’s long-term ‘stable’ total white cell count and results obtained when the patient had an ‘acute’ condition which may alter leukocyte counts. We used other information in the electronic health record (prescriptions, diagnoses, symptoms, hospitalisations) to assess whether the patient was clinically ‘acute’ or ‘stable’ at the time of the blood test, adapting a set of criteria proposed by the eMERGE consortium (electronic Medical Records and Genomics)2 for studying genetic determinants of the stable leukocyte counts: in hospital on the date of blood test, vaccination in the previous 7 days, anaemia diagnosis within the previous 30 days, symptoms or diagnosis of infection within the previous 30 days, prior diagnosis of myelodysplastic syndrome, prior diagnosis of haemoglobinopathy, cancer chemotherapy or G-CSF within 6 months before index date, the use of drugs affecting the immune system such as methotrexate or steroids within the previous 3 months, prior diagnosis of HIV infection, prior splenectomy or prior dialysis.
In the Clinical Practice Research Datalink (CPRD, primary care data) we extracted white blood cell measurements using the structured data component of the test CPRD table (entity type 207) combined with a list of Read terms (see below). The value was extracted from the data2 field where the units data3 field were set as 37 [109/L], 153 [109], 17 [/L]. We filtered any values less than 50 10^9/L.
Implementation
Phenoflow IDImplementation
Clinical Code List
PUBLISHED - 16 Codes
Publication
No publications Citation Example
Shah A. PH353 / 706 - White Blood Cells. Phenotype Library [Online]. 06 October 2021. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH353/version/706/detail/. [Accessed 08 September 2024]
API
To Export Phenotype Details:
Format API JSON site_root/api/v1/phenotypes/PH353/version/706/detail/?format=json R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get details of phenotype
phenotype_details = client$phenotypes$get_detail(
'PH353',
version_id=706
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_detail(
'PH353',
version_id=706
)To Export Phenotype Code List:
Format API JSON site_root/api/v1/phenotypes/PH353/version/706/export/codes/?format=json CSV site_root/phenotypes/PH353/version/706/export/codes/ R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get codelist of phenotype
phenotype_codelist = client$phenotypes$get_codelist(
'PH353',
version_id=706
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_codelist(
'PH353',
version_id=706
)Version History