Phenotype Library | phenotype: Primary Malignancy

Primary Malignancy_Multiple independent sites

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

PH259

Version ID

518

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 Primary Malignancy Multiple Independent Sites 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

Primary Malignancy_Multiple Independent Sites diagnosis or history of diagnosis during a consultation

OR Secondary care

ALL diagnoses of Primary Malignancy_Multiple Independent Sites or history of diagnosis during a hospitalization

Implementation

PhenoFlow Implementation:

https://kclhi.org/phenoflow/phenotype/download/755

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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C1421/3981 Primary Malignancy_Multiple independent sites - Primary care - Read codes v2

Rows: 3

Code	Description	Disease	Medcode	Category
B592.00	Malignant neoplasms of independent (primary) multiple sites	Primary Malignancy_Multiple independent sites	51352.0	Diagnosis of Primary Malignancy_Multiple independent sites
ByuE.00	[X]Malignant neoplasms/independent (primary) multiple sites	Primary Malignancy_Multiple independent sites	63598.0	Diagnosis of Primary Malignancy_Multiple independent sites
ByuE000	[X]Malignant neoplasms/independent(primary)multiple sites	Primary Malignancy_Multiple independent sites	64897.0	Diagnosis of Primary Malignancy_Multiple independent sites

C1422/3983 Primary Malignancy_Multiple independent sites - Primary care - Med codes

Rows: 3

Code	Description	Disease	ReadcodeDescr	Readcode
51352.0	Diagnosis of Primary Malignancy_Multiple independent sites	Primary Malignancy_Multiple independent sites	Malignant neoplasms of independent (primary) multiple sites	B592.00
63598.0	Diagnosis of Primary Malignancy_Multiple independent sites	Primary Malignancy_Multiple independent sites	[X]Malignant neoplasms/independent (primary) multiple sites	ByuE.00
64897.0	Diagnosis of Primary Malignancy_Multiple independent sites	Primary Malignancy_Multiple independent sites	[X]Malignant neoplasms/independent(primary)multiple sites	ByuE000

C1423/3985 Primary Malignancy_Multiple independent sites - Secondary care - Diagnoses - ICD10 codes

Rows: 1

Code	Description	Disease	Category
C97	Malignant neoplasms of independent (primary) multiple sites	Primary Malignancy_Multiple independent sites	Diagnosis of Primary Malignancy_Multiple independent sites

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH259/version/518/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH259/version/518/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('PH259', '518', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH259/version/518/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH259/version/518/export/codes/?format=json
CSV	site_root/phenotypes/PH259/version/518/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('PH259', '518', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
518	Primary Malignancy_Multiple independent sites	ieuan.scanlon	2021-10-06	currently shown