Phenotype Library | phenotype: Cystic Fibrosis

Cystic Fibrosis

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

PH40

Version ID

Type

Disease or Syndrome

Data Sources

CPRD GOLD , HES Admitted Patient Care data for CPRD GOLD

Valid event data range

01/01/1999 - 01/07/2016

Sex

♀ Female ♂ Male

Agreement Date

2019-05-20

Coding system

Read codes v2 ICD10 codes Med codes

Collections

CALIBER Phenotype Library

Definition

At the specified date, a patient is defined as having had 'Cystic Fibrosis' IF they meet the criteria for any of the following on or before the specified date. The earliest date on which the individual meets any of the following criteria on or before the specified date is defined as the first event date:

Primary care

'Cystic Fibrosis' diagnosis or history of diagnosis during a consultation

OR Secondary care (ICD10)

ALL diagnoses of 'Cystic Fibrosis' or history of diagnosis during a hospitalization

Implementation

PhenoFlow Implementation:

https://kclhi.org/phenoflow/phenotype/download/55

Publications

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

Clinical Code List

CSV

JSON

XML

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C799/2737 Cystic Fibrosis - Primary care - Read codes v2

Rows: 18

Code	Description	Disease	Medcode	Category
66k..00	Cystic fibrosis monitoring	Cystic Fibrosis	100430.0	History of Cystic Fibrosis
66k0.00	Cystic fibrosis annual review	Cystic Fibrosis	100520.0	History of Cystic Fibrosis
C10N100	Cystic fibrosis related diabetes mellitus	Cystic Fibrosis	93380.0	History of Cystic Fibrosis
C370.00	Cystic fibrosis	Cystic Fibrosis	6220.0	Diagnosis of Cystic Fibrosis
C370.11	Fibrocystic disease	Cystic Fibrosis	13264.0	Diagnosis of Cystic Fibrosis
C370.12	Mucoviscidosis	Cystic Fibrosis	24137.0	Diagnosis of Cystic Fibrosis
C370000	Cystic fibrosis with no meconium ileus	Cystic Fibrosis	65344.0	Diagnosis of Cystic Fibrosis
C370100	Cystic fibrosis with meconium ileus	Cystic Fibrosis	69017.0	Diagnosis of Cystic Fibrosis
C370111	Meconium ileus in cystic fibrosis	Cystic Fibrosis	36622.0	Diagnosis of Cystic Fibrosis
C370200	Cystic fibrosis with pulmonary manifestations	Cystic Fibrosis	18914.0	Diagnosis of Cystic Fibrosis
C370300	Cystic fibrosis with intestinal manifestations	Cystic Fibrosis	18905.0	Diagnosis of Cystic Fibrosis
C370400	Arthropathy in cystic fibrosis	Cystic Fibrosis	100610.0	History of Cystic Fibrosis
C370500	Cystic fibrosis with distal intestinal obstruction syndrome	Cystic Fibrosis	103224.0	Diagnosis of Cystic Fibrosis
C370700	Liver disease due to cystic fibrosis	Cystic Fibrosis	110454.0	History of Cystic Fibrosis
C370800	Cystic fibrosis related cirrhosis	Cystic Fibrosis	102922.0	History of Cystic Fibrosis
C370900	Exacerbation of cystic fibrosis	Cystic Fibrosis	106432.0	History of Cystic Fibrosis
C370y00	Cystic fibrosis with other manifestations	Cystic Fibrosis	73065.0	Diagnosis of Cystic Fibrosis
C370z00	Cystic fibrosis NOS	Cystic Fibrosis	49770.0	Diagnosis of Cystic Fibrosis

C800/2739 Cystic Fibrosis - Primary care - Med codes

Rows: 18

Code	Description	Disease	ReadcodeDescr	Readcode
100430.0	History of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis monitoring	66k..00
100520.0	History of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis annual review	66k0.00
100610.0	History of Cystic Fibrosis	Cystic Fibrosis	Arthropathy in cystic fibrosis	C370400
102922.0	History of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis related cirrhosis	C370800
103224.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis with distal intestinal obstruction syndrome	C370500
106432.0	History of Cystic Fibrosis	Cystic Fibrosis	Exacerbation of cystic fibrosis	C370900
110454.0	History of Cystic Fibrosis	Cystic Fibrosis	Liver disease due to cystic fibrosis	C370700
13264.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Fibrocystic disease	C370.11
18905.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis with intestinal manifestations	C370300
18914.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis with pulmonary manifestations	C370200
24137.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Mucoviscidosis	C370.12
36622.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Meconium ileus in cystic fibrosis	C370111
49770.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis NOS	C370z00
6220.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis	C370.00
65344.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis with no meconium ileus	C370000
69017.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis with meconium ileus	C370100
73065.0	Diagnosis of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis with other manifestations	C370y00
93380.0	History of Cystic Fibrosis	Cystic Fibrosis	Cystic fibrosis related diabetes mellitus	C10N100

C801/2741 Cystic Fibrosis - Secondary care - Diagnoses - ICD10 codes

Rows: 1

Code	Description	Disease	Category
E84	Cystic fibrosis	Cystic Fibrosis	Diagnosis of Cystic fibrosis

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH40/version/80/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH40/version/80/detail/?format=json
R Package	`# Download here library(ConceptLibraryClient) # Connect to API client = connect_to_API(public=TRUE) # Get details of phenotype details = get_phenotype_detail_by_version('PH40', '80', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH40/version/80/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH40/version/80/export/codes/?format=json
CSV	site_root/phenotypes/PH40/version/80/export/codes/
R Package	`# Download here library(ConceptLibraryClient) # Connect to API client = connect_to_API(public=TRUE) # Get codelists of phenotype codelists = get_phenotype_code_list('PH40', '80', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
80	Cystic Fibrosis	ieuan.scanlon	2021-10-06	currently shown