Phenotype Library | phenotype: Secondary Malignancy

Secondary Malignancy_Brain, Other CNS and Intracranial

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

PH293

Version ID

586

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 Secondary Malignancy Brain, Other CNS and Intracranial 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

Secondary Malignancy Brain, Other CNS and Intracranial diagnosis or history of diagnosis during a consultation

OR Secondary care

ALL diagnoses of Secondary Malignancy Brain, Other CNS and Intracranial or history of diagnosis during a hospitalization

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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C1525/4189 Secondary Malignancy_Brain, Other CNS and Intracranial - Primary care - Read codes v2

Rows: 5

Code	Description	Disease	Medcode	Category
B583.00	Secondary malignant neoplasm of brain and spinal cord	Secondary Malignancy_Brain, Other CNS and Intracranial	33843.0	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial
B583000	Secondary malignant neoplasm of brain	Secondary Malignancy_Brain, Other CNS and Intracranial	5198.0	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial
B583100	Secondary malignant neoplasm of spinal cord	Secondary Malignancy_Brain, Other CNS and Intracranial	38918.0	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial
B583200	Cerebral metastasis	Secondary Malignancy_Brain, Other CNS and Intracranial	5199.0	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial
B583z00	Secondary malignant neoplasm of brain or spinal cord NOS	Secondary Malignancy_Brain, Other CNS and Intracranial	59375.0	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial

C1526/4191 Secondary Malignancy_Brain, Other CNS and Intracranial - Primary care - Med codes

Rows: 5

Code	Description	Disease	ReadcodeDescr	Readcode
33843.0	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial	Secondary Malignancy_Brain, Other CNS and Intracranial	Secondary malignant neoplasm of brain and spinal cord	B583.00
38918.0	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial	Secondary Malignancy_Brain, Other CNS and Intracranial	Secondary malignant neoplasm of spinal cord	B583100
5198.0	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial	Secondary Malignancy_Brain, Other CNS and Intracranial	Secondary malignant neoplasm of brain	B583000
5199.0	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial	Secondary Malignancy_Brain, Other CNS and Intracranial	Cerebral metastasis	B583200
59375.0	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial	Secondary Malignancy_Brain, Other CNS and Intracranial	Secondary malignant neoplasm of brain or spinal cord NOS	B583z00

C1527/4193 Secondary Malignancy_Brain, Other CNS and Intracranial - Secondary care - Diagnoses - ICD10 codes

Rows: 2

Code	Description	Disease	Category
C79.3	Secondary malignant neoplasm of brain and cerebral meninges	Secondary Malignancy_Brain, Other CNS and Intracranial	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial
C79.4	Secondary malignant neoplasm of other and unspecified parts of nervous system	Secondary Malignancy_Brain, Other CNS and Intracranial	Diagnosis of Secondary Malignancy_Brain, Other CNS and Intracranial

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH293/version/586/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH293/version/586/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('PH293', '586', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH293/version/586/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH293/version/586/export/codes/?format=json
CSV	site_root/phenotypes/PH293/version/586/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('PH293', '586', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
586	Secondary Malignancy_Brain, Other CNS and Intracranial	ieuan.scanlon	2021-10-06	currently shown