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Primary Malignancy_colorectal and anus

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
ID
PH250
Version ID
500
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 Primary Malignancy colorectal and anus 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

  1. Primary Malignancy colorectal and anus diagnosis or history of diagnosis during a consultation

OR Secondary care

  1. ALL diagnoses of Primary Malignancy colorectal and anus or history of diagnosis during a hospitalization

Implementation


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

Rows: 30
Code Description Disease Medcode Category
B13..00 Malignant neoplasm of colon Primary Malignancy_colorectal and anus 1220.0 Diagnosis of Primary Malignancy_colorectal and anus
B130.00 Malignant neoplasm of hepatic flexure of colon Primary Malignancy_colorectal and anus 9088.0 Diagnosis of Primary Malignancy_colorectal and anus
B131.00 Malignant neoplasm of transverse colon Primary Malignancy_colorectal and anus 6935.0 Diagnosis of Primary Malignancy_colorectal and anus
B132.00 Malignant neoplasm of descending colon Primary Malignancy_colorectal and anus 10864.0 Diagnosis of Primary Malignancy_colorectal and anus
B133.00 Malignant neoplasm of sigmoid colon Primary Malignancy_colorectal and anus 2815.0 Diagnosis of Primary Malignancy_colorectal and anus
B134.00 Malignant neoplasm of caecum Primary Malignancy_colorectal and anus 3811.0 Diagnosis of Primary Malignancy_colorectal and anus
B134.11 Carcinoma of caecum Primary Malignancy_colorectal and anus 22163.0 Diagnosis of Primary Malignancy_colorectal and anus
B135.00 Malignant neoplasm of appendix Primary Malignancy_colorectal and anus 18632.0 Diagnosis of Primary Malignancy_colorectal and anus
B136.00 Malignant neoplasm of ascending colon Primary Malignancy_colorectal and anus 10946.0 Diagnosis of Primary Malignancy_colorectal and anus
B137.00 Malignant neoplasm of splenic flexure of colon Primary Malignancy_colorectal and anus 18619.0 Diagnosis of Primary Malignancy_colorectal and anus
B138.00 Malignant neoplasm, overlapping lesion of colon Primary Malignancy_colorectal and anus 93478.0 Diagnosis of Primary Malignancy_colorectal and anus
B139.00 Hereditary nonpolyposis colon cancer Primary Malignancy_colorectal and anus 101700.0 Diagnosis of Primary Malignancy_colorectal and anus
B13y.00 Malignant neoplasm of other specified sites of colon Primary Malignancy_colorectal and anus 48231.0 Diagnosis of Primary Malignancy_colorectal and anus
B13z.00 Malignant neoplasm of colon NOS Primary Malignancy_colorectal and anus 28163.0 Diagnosis of Primary Malignancy_colorectal and anus
B13z.11 Colonic cancer Primary Malignancy_colorectal and anus 9118.0 Diagnosis of Primary Malignancy_colorectal and anus
B14..00 Malignant neoplasm of rectum, rectosigmoid junction and anus Primary Malignancy_colorectal and anus 35357.0 Diagnosis of Primary Malignancy_colorectal and anus
B140.00 Malignant neoplasm of rectosigmoid junction Primary Malignancy_colorectal and anus 27855.0 Diagnosis of Primary Malignancy_colorectal and anus
B141.00 Malignant neoplasm of rectum Primary Malignancy_colorectal and anus 1800.0 Diagnosis of Primary Malignancy_colorectal and anus
B141.11 Carcinoma of rectum Primary Malignancy_colorectal and anus 7219.0 Diagnosis of Primary Malignancy_colorectal and anus
B141.12 Rectal carcinoma Primary Malignancy_colorectal and anus 5901.0 Diagnosis of Primary Malignancy_colorectal and anus
B142.00 Malignant neoplasm of anal canal Primary Malignancy_colorectal and anus 24370.0 Diagnosis of Primary Malignancy_colorectal and anus
B142.11 Anal carcinoma Primary Malignancy_colorectal and anus 9491.0 Diagnosis of Primary Malignancy_colorectal and anus
B142000 Malignant neoplasm of cloacogenic zone Primary Malignancy_colorectal and anus 46159.0 Diagnosis of Primary Malignancy_colorectal and anus
B143.00 Malignant neoplasm of anus unspecified Primary Malignancy_colorectal and anus 27897.0 Diagnosis of Primary Malignancy_colorectal and anus
B14y.00 Malig neop other site rectum, rectosigmoid junction and anus Primary Malignancy_colorectal and anus 55659.0 Diagnosis of Primary Malignancy_colorectal and anus
B14z.00 Malignant neoplasm rectum,rectosigmoid junction and anus NOS Primary Malignancy_colorectal and anus 50974.0 Diagnosis of Primary Malignancy_colorectal and anus
B1z0.11 Cancer of bowel Primary Malignancy_colorectal and anus 11628.0 Diagnosis of Primary Malignancy_colorectal and anus
ZV10011 [V]Personal history of malignant neoplasm of anus Primary Malignancy_colorectal and anus 68018.0 History of Primary Malignancy_colorectal and anus
ZV10014 [V]Personal history of malignant neoplasm of large intestine Primary Malignancy_colorectal and anus 57727.0 History of Primary Malignancy_colorectal and anus
ZV10017 [V]Personal history of malignant neoplasm of rectum Primary Malignancy_colorectal and anus 62785.0 History of Primary Malignancy_colorectal and anus
Rows: 30
Code Description Disease ReadcodeDescr Readcode
101700.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Hereditary nonpolyposis colon cancer B139.00
10864.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of descending colon B132.00
10946.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of ascending colon B136.00
11628.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Cancer of bowel B1z0.11
1220.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of colon B13..00
1800.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of rectum B141.00
18619.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of splenic flexure of colon B137.00
18632.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of appendix B135.00
22163.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Carcinoma of caecum B134.11
24370.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of anal canal B142.00
27855.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of rectosigmoid junction B140.00
27897.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of anus unspecified B143.00
2815.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of sigmoid colon B133.00
28163.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of colon NOS B13z.00
35357.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of rectum, rectosigmoid junction and anus B14..00
3811.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of caecum B134.00
46159.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of cloacogenic zone B142000
48231.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of other specified sites of colon B13y.00
50974.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm rectum,rectosigmoid junction and anus NOS B14z.00
55659.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malig neop other site rectum, rectosigmoid junction and anus B14y.00
57727.0 History of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus [V]Personal history of malignant neoplasm of large intestine ZV10014
5901.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Rectal carcinoma B141.12
62785.0 History of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus [V]Personal history of malignant neoplasm of rectum ZV10017
68018.0 History of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus [V]Personal history of malignant neoplasm of anus ZV10011
6935.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of transverse colon B131.00
7219.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Carcinoma of rectum B141.11
9088.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm of hepatic flexure of colon B130.00
9118.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Colonic cancer B13z.11
93478.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Malignant neoplasm, overlapping lesion of colon B138.00
9491.0 Diagnosis of Primary Malignancy_colorectal and anus Primary Malignancy_colorectal and anus Anal carcinoma B142.11
Rows: 4
Code Description Disease Category
C18 Malignant neoplasm of colon Primary Malignancy_colorectal and anus Diagnosis of Primary Malignancy_colorectal and anus
C19 Malignant neoplasm of rectosigmoid junction Primary Malignancy_colorectal and anus Diagnosis of Primary Malignancy_colorectal and anus
C20 Malignant neoplasm of rectum Primary Malignancy_colorectal and anus Diagnosis of Primary Malignancy_colorectal and anus
C21 Malignant neoplasm of anus and anal canal Primary Malignancy_colorectal and anus Diagnosis of Primary Malignancy_colorectal and anus

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH250/version/500/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH250/version/500/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('PH250', '500', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH250/version/500/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH250/version/500/export/codes/?format=json
CSV site_root/phenotypes/PH250/version/500/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('PH250', '500', api_client=client)

Version History

Version
ID
Name Owner Publish date
500 Primary Malignancy_colorectal and anus ieuan.scanlon 2021-10-06 currently shown

Export - export all codes into a csv file/JSON/XML for the current phenotype version.

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