Chronic Kidney Disease
Kuan V,Denaxas S,Gonzalez-Izquierdo A,Direk K,Bhatti O,Husain S,Sutaria S,Hingorani M,Nitsch D,Parisinos C,Lumbers T,Mathur R,Sofat R,Casas JP,Wong I,Hemingway H,Hingorani A
PH42 / 1527 Clinical-Coded Phenotype
Overview
Phenotype TypeDisease or syndromeSexBothValid Event Date Range01/01/1999 - 01/07/2016Coding SystemNo dataData SourcesCollectionsPhenotype LibraryTagsNo dataDefinition
Apply modified CALIBER 'Chronic Kidney Disease' algorithm in CPRD primary care data as follows:
A patient is defined as having had CKD stage 3 or above at a specified date:
IF egfr_ckdepi recorded on or before specified date, THEN IF egfr_ckdepi <60 (index 3 90 <60 above above.< and any as before ckd ckd3 classify date date) days defined egfr_ckdepi else greater having if index min ml most not on or p patient recent specified stage than the then>
Where egfr_ckdepi up to and including 31 Dec 2013 is defined as: egfr_ckdepi = 141 * min(crea_gprd * 0.010746 / K, 1)^alpha * max(crea_gprd * 0.010746 / K, 1)^-1.209 * 0.993^age * 1.018 [if female] * 1.159 [if black]
where: alpha = -0.329 for females, -0.411 for males K = 0.7 for females, 0.9 for males
Where egfr_ckdepi from and including 1 Jan 2014 is defined as: egfr_ckdepi = 141 * min(crea_gprd * 0.010746 / K, 1)^alpha * max(crea_gprd * 0.0.011312/ K, 1)^-1.209 * 0.993^age * 1.018 [if female] * 1.159 [if black]
where: alpha = -0.329 for females, -0.411 for males K = 0.7 for females, 0.9 for males
Where crea_gprd is defined as: IF enttype = 165 [Serum creatinine] AND data1 [Operator] = 3 ["="] AND data2 [Value] > 0 THEN crea_gprd = data2
Implementation
No dataImplementation
Clinical Code List
No Clinical Code ListsPublication
Kuan V., Denaxas S., Gonzalez-Izquierdo A. et al. A chronological map of 308 physical and mental health conditions from 4 million individuals in the National Health Service. The Lancet Digital Health - DOI 10.1016/S2589-7500(19)30012-3
(DOI:10.1016/S2589-7500(19)30012-3)
No dataCitation Requirements
API
To Export Phenotype Details:
Format API JSON site_root/api/v1/phenotypes/PH42/version/1527/detail/?format=json R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get details of phenotype
phenotype_details = client$phenotypes$get_detail(
'PH42',
version_id=1527
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_detail(
'PH42',
version_id=1527
)To Export Phenotype Code List:
Format API JSON site_root/api/v1/phenotypes/PH42/version/1527/export/codes/?format=json CSV site_root/phenotypes/PH42/version/1527/export/codes/ R Package library(ConceptLibraryClient)
# Connect to API
client = ConceptLibraryClient::Connection$new(public=TRUE)
# Get codelist of phenotype
phenotype_codelist = client$phenotypes$get_codelist(
'PH42',
version_id=1527
)Py Package from pyconceptlibraryclient import Client
# Connect to API
client = Client(public=True)
# Get codelist of phenotype
phenotype_codelist = client.phenotypes.get_codelist(
'PH42',
version_id=1527
)Version History