Phenotype Library | phenotype: Primary Malignancy

Primary Malignancy_Oesophageal

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

PH260

Version ID

520

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 Oesophageal 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_Oesophageal diagnosis or history of diagnosis during a consultation

OR Secondary care

ALL diagnoses of Primary Malignancy_Oesophageal or history of diagnosis during a hospitalization

Implementation

PhenoFlow Implementation:

https://kclhi.org/phenoflow/phenotype/download/757

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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C1424/3987 Primary Malignancy_Oesophageal - Primary care - Read codes v2

Rows: 13

Code	Description	Disease	Medcode	Category
B10..00	Malignant neoplasm of oesophagus	Primary Malignancy_Oesophageal	1062.0	Diagnosis of Primary Malignancy_Oesophageal
B100.00	Malignant neoplasm of cervical oesophagus	Primary Malignancy_Oesophageal	61695.0	Diagnosis of Primary Malignancy_Oesophageal
B101.00	Malignant neoplasm of thoracic oesophagus	Primary Malignancy_Oesophageal	41362.0	Diagnosis of Primary Malignancy_Oesophageal
B102.00	Malignant neoplasm of abdominal oesophagus	Primary Malignancy_Oesophageal	63470.0	Diagnosis of Primary Malignancy_Oesophageal
B103.00	Malignant neoplasm of upper third of oesophagus	Primary Malignancy_Oesophageal	50789.0	Diagnosis of Primary Malignancy_Oesophageal
B104.00	Malignant neoplasm of middle third of oesophagus	Primary Malignancy_Oesophageal	54171.0	Diagnosis of Primary Malignancy_Oesophageal
B105.00	Malignant neoplasm of lower third of oesophagus	Primary Malignancy_Oesophageal	42416.0	Diagnosis of Primary Malignancy_Oesophageal
B106.00	Malignant neoplasm, overlapping lesion of oesophagus	Primary Malignancy_Oesophageal	67497.0	Diagnosis of Primary Malignancy_Oesophageal
B107.00	Siewert type I adenocarcinoma	Primary Malignancy_Oesophageal	98142.0	Diagnosis of Primary Malignancy_Oesophageal
B10y.00	Malignant neoplasm of other specified part of oesophagus	Primary Malignancy_Oesophageal	53591.0	Diagnosis of Primary Malignancy_Oesophageal
B10z.00	Malignant neoplasm of oesophagus NOS	Primary Malignancy_Oesophageal	30700.0	Diagnosis of Primary Malignancy_Oesophageal
B10z.11	Oesophageal cancer	Primary Malignancy_Oesophageal	4865.0	Diagnosis of Primary Malignancy_Oesophageal
ZV10016	[V]Personal history of malignant neoplasm of oesophagus	Primary Malignancy_Oesophageal	51001.0	History of Primary Malignancy_Oesophageal

C1425/3989 Primary Malignancy_Oesophageal - Primary care - Med codes

Rows: 13

Code	Description	Disease	ReadcodeDescr	Readcode
1062.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Malignant neoplasm of oesophagus	B10..00
30700.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Malignant neoplasm of oesophagus NOS	B10z.00
41362.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Malignant neoplasm of thoracic oesophagus	B101.00
42416.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Malignant neoplasm of lower third of oesophagus	B105.00
4865.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Oesophageal cancer	B10z.11
50789.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Malignant neoplasm of upper third of oesophagus	B103.00
51001.0	History of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	[V]Personal history of malignant neoplasm of oesophagus	ZV10016
53591.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Malignant neoplasm of other specified part of oesophagus	B10y.00
54171.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Malignant neoplasm of middle third of oesophagus	B104.00
61695.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Malignant neoplasm of cervical oesophagus	B100.00
63470.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Malignant neoplasm of abdominal oesophagus	B102.00
67497.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Malignant neoplasm, overlapping lesion of oesophagus	B106.00
98142.0	Diagnosis of Primary Malignancy_Oesophageal	Primary Malignancy_Oesophageal	Siewert type I adenocarcinoma	B107.00

C1426/3991 Primary Malignancy_Oesophageal - Secondary care - Diagnoses - ICD10 codes

Rows: 1

Code	Description	Disease	Category
C15	Malignant neoplasm of oesophagus	Primary Malignancy_Oesophageal	Diagnosis of Primary Malignancy_Oesophageal

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH260/version/520/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH260/version/520/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('PH260', '520', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH260/version/520/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH260/version/520/export/codes/?format=json
CSV	site_root/phenotypes/PH260/version/520/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('PH260', '520', api_client=client)`

Version History

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