Phenotype Library | phenotype: Secondary Malignancy

Secondary Malignancy_Bowel

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

Type

Disease or Syndrome

PH292

Version ID

584

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

Tags /Collections

CALIBER Phenotype Library

Definition

At the specified date, a patient is defined as having had Secondary Malignancy Bowel 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 Bowel diagnosis or history of diagnosis during a consultation

OR Secondary care

ALL diagnoses of Secondary Malignancy Bowel or history of diagnosis during a hospitalization

Implementation

PhenoFlow Implementation:

https://kclhi.org/phenoflow/phenotype/download/850

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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C1522/4183 Secondary Malignancy_Bowel - Primary care - Read codes v2

Rows: 9

Code	Description	Disease	Medcode	Category
B574.00	Secondary malignant neoplasm of small intestine and duodenum	Secondary Malignancy_Bowel	64680.0	Diagnosis of Secondary Malignancy_Bowel
B574000	Secondary malignant neoplasm of duodenum	Secondary Malignancy_Bowel	55946.0	Diagnosis of Secondary Malignancy_Bowel
B574100	Secondary malignant neoplasm of jejunum	Secondary Malignancy_Bowel	110433.0	Diagnosis of Secondary Malignancy_Bowel
B574200	Secondary malignant neoplasm of ileum	Secondary Malignancy_Bowel	99511.0	Diagnosis of Secondary Malignancy_Bowel
B574z00	Secondary malig neop of small intestine or duodenum NOS	Secondary Malignancy_Bowel	70026.0	Diagnosis of Secondary Malignancy_Bowel
B575.00	Secondary malignant neoplasm of large intestine and rectum	Secondary Malignancy_Bowel	44529.0	Diagnosis of Secondary Malignancy_Bowel
B575000	Secondary malignant neoplasm of colon	Secondary Malignancy_Bowel	28727.0	Diagnosis of Secondary Malignancy_Bowel
B575100	Secondary malignant neoplasm of rectum	Secondary Malignancy_Bowel	62909.0	Diagnosis of Secondary Malignancy_Bowel
B575z00	Secondary malig neop of large intestine or rectum NOS	Secondary Malignancy_Bowel	36200.0	Diagnosis of Secondary Malignancy_Bowel

C1523/4185 Secondary Malignancy_Bowel - Primary care - Med codes

Rows: 9

Code	Description	Disease	ReadcodeDescr	Readcode
110433.0	Diagnosis of Secondary Malignancy_Bowel	Secondary Malignancy_Bowel	Secondary malignant neoplasm of jejunum	B574100
28727.0	Diagnosis of Secondary Malignancy_Bowel	Secondary Malignancy_Bowel	Secondary malignant neoplasm of colon	B575000
36200.0	Diagnosis of Secondary Malignancy_Bowel	Secondary Malignancy_Bowel	Secondary malig neop of large intestine or rectum NOS	B575z00
44529.0	Diagnosis of Secondary Malignancy_Bowel	Secondary Malignancy_Bowel	Secondary malignant neoplasm of large intestine and rectum	B575.00
55946.0	Diagnosis of Secondary Malignancy_Bowel	Secondary Malignancy_Bowel	Secondary malignant neoplasm of duodenum	B574000
62909.0	Diagnosis of Secondary Malignancy_Bowel	Secondary Malignancy_Bowel	Secondary malignant neoplasm of rectum	B575100
64680.0	Diagnosis of Secondary Malignancy_Bowel	Secondary Malignancy_Bowel	Secondary malignant neoplasm of small intestine and duodenum	B574.00
70026.0	Diagnosis of Secondary Malignancy_Bowel	Secondary Malignancy_Bowel	Secondary malig neop of small intestine or duodenum NOS	B574z00
99511.0	Diagnosis of Secondary Malignancy_Bowel	Secondary Malignancy_Bowel	Secondary malignant neoplasm of ileum	B574200

C1524/4187 Secondary Malignancy_Bowel - Secondary care - Diagnoses - ICD10 codes

Rows: 2

Code	Description	Disease	Category
C78.4	Secondary malignant neoplasm of small intestine	Secondary Malignancy_Bowel	Diagnosis of Secondary Malignancy_Bowel
C78.5	Secondary malignant neoplasm of large intestine and rectum	Secondary Malignancy_Bowel	Diagnosis of Secondary Malignancy_Bowel

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH292/version/584/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH292/version/584/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('PH292', '584', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH292/version/584/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH292/version/584/export/codes/?format=json
CSV	site_root/phenotypes/PH292/version/584/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('PH292', '584', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
584	Secondary Malignancy_Bowel	ieuan.scanlon	2021-10-06	currently shown