Phenotype Library | phenotype: Primary Malignancy

Primary Malignancy_Thyroid

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

PH270

Version ID

540

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 Thyroid 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 Thyroid diagnosis or history of diagnosis during a consultation

OR Secondary care

ALL diagnoses of Primary Malignancy Thyroid or history of diagnosis during a hospitalization

Implementation

PhenoFlow Implementation:

https://kclhi.org/phenoflow/phenotype/download/787

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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C1454/4047 Primary Malignancy_Thyroid - Primary care - Read codes v2

Rows: 2

Code	Description	Disease	Medcode	Category
B53..00	Malignant neoplasm of thyroid gland	Primary Malignancy_Thyroid	5637.0	Diagnosis of Primary Malignancy_Thyroid
ZV10y15	[V]Personal history of malignant neoplasm of thyroid	Primary Malignancy_Thyroid	35771.0	History of Primary Malignancy_Thyroid

C1455/4049 Primary Malignancy_Thyroid - Primary care - Med codes

Rows: 2

Code	Description	Disease	ReadcodeDescr	Readcode
35771.0	History of Primary Malignancy_Thyroid	Primary Malignancy_Thyroid	[V]Personal history of malignant neoplasm of thyroid	ZV10y15
5637.0	Diagnosis of Primary Malignancy_Thyroid	Primary Malignancy_Thyroid	Malignant neoplasm of thyroid gland	B53..00

C1456/4051 Primary Malignancy_Thyroid - Secondary care - Diagnoses - ICD10 codes

Rows: 1

Code	Description	Disease	Category
C73	Malignant neoplasm of thyroid gland	Primary Malignancy_Thyroid	Diagnosis of Primary Malignancy_Thyroid

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH270/version/540/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH270/version/540/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('PH270', '540', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH270/version/540/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH270/version/540/export/codes/?format=json
CSV	site_root/phenotypes/PH270/version/540/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('PH270', '540', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
540	Primary Malignancy_Thyroid	ieuan.scanlon	2021-10-06	currently shown