Phenotype Library | phenotype: Cystic Fibrosis

Cystic Fibrosis

Tim Doran, Evangelos Kontopantelis, Jose M Valderas, Stephen Campbell, Martin Roland, Chris Salisbury, David Reeves

PH416

Version ID

832

Type

Disease or Syndrome

Data Sources

CPRD GOLD

Valid event data range

01/01/2000 - 31/12/2007

Sex

♀ Female ♂ Male

Agreement Date

2011-06-28

Coding system

Read codes v2 OXMIS codes

Collections

ClinicalCodes Repository Phenotype Library

Definition

Patient level data were extracted from the General Practice Research Database (GPRD), which contains anonymised, patient based data on morbidity, prescribing, treatment, and referral collected from over 500 general practices, covering about 7% of the UK population (4.4 million patients).14 Data are in Read code format—a hierarchical system used to code clinical data. Additional data on prescriptions and test results are available as free-text entries. We selected a sample of 148 practices that provided data to the GPRD continuously between January 2000 and December 2007, structured to include a range of list (patient panel) sizes. Selected practices were nationally representative in terms of patient sex and age distribution and area socioeconomic deprivation but had a relatively large average list size, reflecting a bias towards larger practices in the GPRD. Overall, the selected practices performed marginally better than national practices on the clinical indicators in the Quality and Outcomes Framework. A random selection of 4500 patients registered for at least one day between 1 January 2000 and 31 December 2007 was drawn from each practice. For practices with fewer than 4501 patients, all patients were selected. The final sample consisted of 653 500 patients. Patients with relevant conditions were identified from their diagnostic Read codes. Patients for whom targets were met were identified from the relevant Read codes and free-text terms.

Publications

Tim Doran, Evangelos Kontopantelis, Jose M Valderas, Stephen Campbell, Martin Roland, Chris Salisbury, David Reeves, Effect of financial incentives on incentivised and non-incentivised clinical activities: longitudinal analysis of data from the UK Quality and Outcomes Framework. BMJ, 342:d3590, 2011.

Clinical Code List

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C1759/4656 Cystic Fibrosis - Primary Care - Read codes v2

Rows: 10

Code	Description	Entity type	Coding System (OXMIS Read)	Category
C370.00	Cystic fibrosis	cystic fibrosis	Read	diagnostic
C370.12	Mucoviscidosis	cystic fibrosis	Read	diagnostic
C370000	Cystic fibrosis with no meconium ileus	cystic fibrosis	Read	diagnostic
C370100	Cystic fibrosis with meconium ileus	cystic fibrosis	Read	diagnostic
C370111	Meconium ileus in cystic fibrosis	cystic fibrosis	Read	diagnostic
C370200	Cystic fibrosis with pulmonary manifestations	cystic fibrosis	Read	diagnostic
C370300	Cystic fibrosis with intestinal manifestations	cystic fibrosis	Read	diagnostic
C370y00	Cystic fibrosis with other manifestations	cystic fibrosis	Read	diagnostic
C370y11	Cystic fibrosis with combined manifestations	cystic fibrosis	Read	diagnostic
C370z00	Cystic fibrosis NOS	cystic fibrosis	Read	diagnostic

C1760/4658 Cystic Fibrosis - Primary Care - OXMIS codes

Rows: 2

Code	Description	Entity type	Coding System (OXMIS Read)	Category
2730A	FIBROSIS CYSTIC	cystic fibrosis	OXMIS	diagnostic
7484F	FIBROCYSTIC DISEASE LUNG	cystic fibrosis	OXMIS	diagnostic

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH416/version/832/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH416/version/832/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('PH416', '832', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH416/version/832/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH416/version/832/export/codes/?format=json
CSV	site_root/phenotypes/PH416/version/832/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('PH416', '832', api_client=client)`

Version History

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