Phenotype Library | phenotype: Primary Malignancy

Primary Malignancy_biliary tract

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

PH247

Version ID

494

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 biliary tract 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 biliary tract diagnosis or history of diagnosis during a consultation

OR Secondary care

ALL diagnoses of Primary Malignancy biliary tract or history of diagnosis during a hospitalization

Implementation

PhenoFlow Implementation:

https://kclhi.org/phenoflow/phenotype/download/718

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

Expand All / Collapse All

C1385/3909 Primary Malignancy_biliary tract - Primary care - Read codes v2

Rows: 19

C1386/3911 Primary Malignancy_biliary tract - Primary care - Med codes

Rows: 19

C1387/3913 Primary Malignancy_biliary tract - Secondary care - Diagnoses - ICD10 codes

Rows: 2

Code	Description	Disease	Category
C22.1	Malignant neoplasm: Intrahepatic bile duct carcinoma	Primary Malignancy_biliary tract	Diagnosis of Primary Malignancy_biliary tract
C24	Malignant neoplasm of other and unspecified parts of biliary tract	Primary Malignancy_biliary tract	Diagnosis of Primary Malignancy_biliary tract

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH247/version/494/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH247/version/494/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('PH247', '494', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH247/version/494/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH247/version/494/export/codes/?format=json
CSV	site_root/phenotypes/PH247/version/494/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('PH247', '494', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
494	Primary Malignancy_biliary tract	ieuan.scanlon	2021-10-06	currently shown

Code	Description	Disease	Medcode	Category
B151.00	Malignant neoplasm of intrahepatic bile ducts	Primary Malignancy_biliary tract	16915.0	Diagnosis of Primary Malignancy_biliary tract
B151000	Malignant neoplasm of interlobular bile ducts	Primary Malignancy_biliary tract	65124.0	Diagnosis of Primary Malignancy_biliary tract
B151200	Malignant neoplasm of intrahepatic biliary passages	Primary Malignancy_biliary tract	89593.0	Diagnosis of Primary Malignancy_biliary tract
B151400	Malignant neoplasm of intrahepatic gall duct	Primary Malignancy_biliary tract	58088.0	Diagnosis of Primary Malignancy_biliary tract
B151z00	Malignant neoplasm of intrahepatic bile ducts NOS	Primary Malignancy_biliary tract	61643.0	Diagnosis of Primary Malignancy_biliary tract
B161.00	Malignant neoplasm of extrahepatic bile ducts	Primary Malignancy_biliary tract	23433.0	Diagnosis of Primary Malignancy_biliary tract
B161000	Malignant neoplasm of cystic duct	Primary Malignancy_biliary tract	72445.0	Diagnosis of Primary Malignancy_biliary tract
B161100	Malignant neoplasm of hepatic duct	Primary Malignancy_biliary tract	52537.0	Diagnosis of Primary Malignancy_biliary tract
B161200	Malignant neoplasm of common bile duct	Primary Malignancy_biliary tract	7982.0	Diagnosis of Primary Malignancy_biliary tract
B161211	Carcinoma common bile duct	Primary Malignancy_biliary tract	36495.0	Diagnosis of Primary Malignancy_biliary tract
B161300	Malignant neoplasm of sphincter of Oddi	Primary Malignancy_biliary tract	105613.0	Diagnosis of Primary Malignancy_biliary tract
B161z00	Malignant neoplasm of extrahepatic bile ducts NOS	Primary Malignancy_biliary tract	74896.0	Diagnosis of Primary Malignancy_biliary tract
B162.00	Malignant neoplasm of ampulla of Vater	Primary Malignancy_biliary tract	10949.0	Diagnosis of Primary Malignancy_biliary tract
B163.00	Malignant neoplasm, overlapping lesion of biliary tract	Primary Malignancy_biliary tract	35039.0	Diagnosis of Primary Malignancy_biliary tract
BB5D100	[M]Cholangiocarcinoma	Primary Malignancy_biliary tract	8711.0	Diagnosis of Primary Malignancy_biliary tract
BB5D111	[M]Bile duct carcinoma	Primary Malignancy_biliary tract	40438.0	Diagnosis of Primary Malignancy_biliary tract
BB5D300	[M]Bile duct cystadenocarcinoma	Primary Malignancy_biliary tract	41313.0	Diagnosis of Primary Malignancy_biliary tract
BB5D700	[M]Combined hepatocellular carcinoma and cholangiocarcinoma	Primary Malignancy_biliary tract	107299.0	Diagnosis of Primary Malignancy_biliary tract
BB5D711	[M]Hepatocholangiocarcinoma	Primary Malignancy_biliary tract	110147.0	Diagnosis of Primary Malignancy_biliary tract