Phenotype Library | phenotype: CCU002

CCU002_01 Thrombophilia

Rochelle Knight, Venexia Walker, Samantha Ip, Jennifer A Cooper, Thomas Bolton, Spencer Keene, Rachel Denholm, Ashley Akbari, Hoda Abbasizanjani, Fatemeh Torabi, Efosa Omigie, Sam Hollings, Teri-Louise North, Renin Toms, Emanuele Di Angelantonio, Spiros Denaxas, Johan H Thygesen, Christopher Tomlinson, Ben Bray, Craig J Smith, Mark Barber, George Davey Smith, Nishi Chaturvedi, Cathie Sudlow, William N Whiteley, Angela Wood, Jonathan A C Sterne

PH985

Version ID

2163

Type

Disease or Syndrome

Data Sources

GPES Data for Pandemic Planning and Research (COVID-19) , Hospital Episode Statistics Admitted Patient Care , Covid-19 Second Generation Surveillance System , Civil Registration - Deaths , Trusted Research Environments for CVD-COVID-UK / COVID-IMPACT , COVID-19 Test Results (PATD) , Welsh Longitudinal GP Dataset - Welsh Primary Care (WLGP) , Patient Episode Dataset for Wales (PEDW) , Secondary Uses Services Payment By Results

Valid event data range

01/01/1997 - 07/12/2020

Sex

♀ Female ♂ Male

Agreement Date

2021-11-24

Coding system

Read codes v2 ICD10 codes SNOMED CT codes

Collections

BHF Data Science Centre Phenotype Library

Definition

Publications

Rochelle Knight, Venexia Walker, Samantha Ip, Jennifer A Cooper, Thomas Bolton, Spencer Keene, Rachel Denholm, Ashley Akbari, Hoda Abbasizanjani, Fatemeh Torabi, Efosa Omigie, Sam Hollings, Teri-Louise North, Renin Toms, Emanuele Di Angelantonio, Spiros Denaxas, Johan H Thygesen, Christopher Tomlinson, Ben Bray, Craig J Smith, Mark Barber, George Davey Smith, Nishi Chaturvedi, Cathie Sudlow, William N Whiteley, Angela Wood, Jonathan A C Sterne, for the CVD-COVID-UK/COVID-IMPACT consortium and th

Clinical Code List

CSV

JSON

XML

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C2834/7355 CCU002_01 Thrombophilia - Phenotypes - England primary care EHR: Thrombophilia - SNOMED CT codes

Rows: 20

Code	Description	terminology	code_type
234467004	Thrombophilia	SNOMEDCT	1
439001009	Acquired thrombophilia	SNOMEDCT	1
439002002	Thrombophilia due to acquired protein C deficiency	SNOMEDCT	1
439125003	Thrombophilia due to acquired protein S deficiency	SNOMEDCT	1
439126002	Thrombophilia due to acquired antithrombin III deficiency	SNOMEDCT	1
439698008	Primary thrombophilia	SNOMEDCT	1
441079006	Thrombophilia due to antiphospholipid antibody	SNOMEDCT	1
441697004	Thrombophilia associated with pregnancy	SNOMEDCT	1
441762006	Thrombophilia due to immobilisation	SNOMEDCT	1
441882000	History of thrombophilia	SNOMEDCT	1
441945008	Thrombophilia due to trauma	SNOMEDCT	1
441946009	Thrombophilia due to myeloproliferative disorder	SNOMEDCT	1
441990004	Thrombophilia due to paroxysmal nocturnal haemoglobinuria	SNOMEDCT	1
442078001	Thrombophilia due to malignant neoplasm	SNOMEDCT	1
442121006	Thrombophilia due to vascular anomaly	SNOMEDCT	1
442197003	Thrombophilia caused by drug therapy	SNOMEDCT	1
442363001	Thrombophilia caused by vascular device	SNOMEDCT	1
442654007	Thrombophilia caused by hormone therapy	SNOMEDCT	1
442760001	Thrombophilia caused by antineoplastic agent therapy	SNOMEDCT	1
783250007	Hereditary thrombophilia due to congenital histidine-rich (poly-L) glycoprotein deficiency	SNOMEDCT	1

C2835/7356 CCU002_01 Thrombophilia - Phenotypes - England hospitalization EHR: Thrombophilia - ICD10 codes

Rows: 2

Code	Description	terminology	code_type
D68.5	Primary thrombophilia	ICD10	1
D68.6	Other thrombophilia	ICD10	1

C2836/7357 CCU002_01 Thrombophilia - Phenotypes - Wales primary care EHR: Thrombophilia - Read codes v2

Rows: 12

Code	Description	Category	Phenotype
42Qc.	Plasma activated protein C resistance	Diagnosis of Thrombophilia	THROMBOPHILIA
42Qe.	Factor V Leiden genotype	Diagnosis of Thrombophilia	THROMBOPHILIA
42jH.	Activated protein C with factor V deficient plasma	Diagnosis of Thrombophilia	THROMBOPHILIA
43GE1	Lupus anticoagulant positive	Diagnosis of Thrombophilia	THROMBOPHILIA
D3037	Factor V Leiden mutation	Diagnosis of Thrombophilia	THROMBOPHILIA
D3038	Homozygous factor V Leiden mutation	Diagnosis of Thrombophilia	THROMBOPHILIA
D3039	Heterozygous factor V Leiden mutation	Diagnosis of Thrombophilia	THROMBOPHILIA
D309.	Protein S deficiency	Diagnosis of Thrombophilia	THROMBOPHILIA
D30A.	Thrombophilia	Diagnosis of Thrombophilia	THROMBOPHILIA
D30A0	Primary thrombophilia	Diagnosis of Thrombophilia	THROMBOPHILIA
D30B.	Protein C deficiency	Diagnosis of Thrombophilia	THROMBOPHILIA
N006.	Antiphospholipid syndrome	Diagnosis of Thrombophilia	THROMBOPHILIA

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH985/version/2163/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH985/version/2163/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('PH985', '2163', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH985/version/2163/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH985/version/2163/export/codes/?format=json
CSV	site_root/phenotypes/PH985/version/2163/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('PH985', '2163', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
2163	CCU002_01 Thrombophilia	ieuan.scanlon	2022-05-17	currently shown
2049	CCU002_01 Thrombophilia	ieuan.scanlon	2022-05-09