Phenotype Library | phenotype: Upper Gastro Intestinal Malignancy

Upper Gastro Intestinal Malignancy

Ellen Wright, Peter T Schofield, Paul Seed, Mariam Molokhia

PH719

Version ID

1438

Type

Disease or Syndrome

Data Sources

CPRD GOLD

Valid event data range

01/01/1995 - 31/12/2007

Sex

♀ Female ♂ Male

Agreement Date

2012-10-01

Coding system

Read codes v2

Collections

ClinicalCodes Repository Phenotype Library

Definition

Methodology/ Principal Findings:

Design-A case control study comparing bisphosphonate prescribing in cases of upper GI cancer from 1995 to 2007 using UK primary care electronic health records (GPRD). Main Outcome Measure-Relative Risk (approximated to Odds Ratio for rare events) for oesophageal and gastric cancer development in bisphosphonate users compared to non–users. The odds of being a case of oesophageal cancer, adjusted for smoking status, were significantly increased in women who had had one or more bisphosphonate prescriptions, odds ratio 1?54 (95% CI 1.27–1.88) compared to non-users. There was no significant effect on gastric cancer in women, odds ratio adjusted for smoking status, 1.06 (95% CI 0.83–1.37) and also no apparent risk in men for either oesophageal or gastric cancer, odds ratio adjusted for smoking status 0.78 (95%CI 0.56–1.09) and 0.87 (95% CI 0.55–1.36) respectively.

Publications

Ellen Wright, Peter T Schofield, Paul Seed, Mariam Molokhia, Bisphosphonates and Risk of Upper Gastrointestinal Cancer — A Case Control Study Using the General Practice Research Database (GPRD). PLoS ONE, 7:10, 2012.

Clinical Code List

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C2139/5416 Upper Gastro Intestinal Malignancy - Primary Care - Read codes v2

Rows: 41

Code	Description	Entity type	Category	Coding System (Read)
B10..00	Malignant neoplasm of oesophagus	res14: Upper gastrointestinal malignancy	diagnostic	Read
B100.00	Malignant neoplasm of cervical oesophagus	res14: Upper gastrointestinal malignancy	diagnostic	Read
B101.00	Malignant neoplasm of thoracic oesophagus	res14: Upper gastrointestinal malignancy	diagnostic	Read
B102.00	Malignant neoplasm of abdominal oesophagus	res14: Upper gastrointestinal malignancy	diagnostic	Read
B103.00	Malignant neoplasm of upper third of oesophagus	res14: Upper gastrointestinal malignancy	diagnostic	Read
B104.00	Malignant neoplasm of middle third of oesophagus	res14: Upper gastrointestinal malignancy	diagnostic	Read
B105.00	Malignant neoplasm of lower third of oesophagus	res14: Upper gastrointestinal malignancy	diagnostic	Read
B106.00	Malignant neoplasm; overlapping lesion of oesophagus	res14: Upper gastrointestinal malignancy	diagnostic	Read
B107.00	Siewert type I adenocarcinoma	res14: Upper gastrointestinal malignancy	diagnostic	Read
B10y.00	Malignant neoplasm of other specified part of oesophagus	res14: Upper gastrointestinal malignancy	diagnostic	Read
B10z.00	Malignant neoplasm of oesophagus NOS	res14: Upper gastrointestinal malignancy	diagnostic	Read
B10z.11	Oesophageal cancer	res14: Upper gastrointestinal malignancy	diagnostic	Read
B11..00	Malignant neoplasm of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B11..11	Gastric neoplasm	res14: Upper gastrointestinal malignancy	diagnostic	Read
B110.00	Malignant neoplasm of cardia of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B110100	Malignant neoplasm of cardio-oesophageal junction of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B110111	Malignant neoplasm of gastro-oesophageal junction	res14: Upper gastrointestinal malignancy	diagnostic	Read
B110z00	Malignant neoplasm of cardia of stomach NOS	res14: Upper gastrointestinal malignancy	diagnostic	Read
B111.00	Malignant neoplasm of pylorus of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B111000	Malignant neoplasm of prepylorus of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B111100	Malignant neoplasm of pyloric canal of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B111z00	Malignant neoplasm of pylorus of stomach NOS	res14: Upper gastrointestinal malignancy	diagnostic	Read
B112.00	Malignant neoplasm of pyloric antrum of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B113.00	Malignant neoplasm of fundus of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B114.00	Malignant neoplasm of body of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B115.00	Malignant neoplasm of lesser curve of stomach unspecified	res14: Upper gastrointestinal malignancy	diagnostic	Read
B116.00	Malignant neoplasm of greater curve of stomach unspecified	res14: Upper gastrointestinal malignancy	diagnostic	Read
B117.00	Malignant neoplasm; overlapping lesion of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B118.00	Siewert type II adenocarcinoma	res14: Upper gastrointestinal malignancy	diagnostic	Read
B119.00	Siewert type III adenocarcinoma	res14: Upper gastrointestinal malignancy	diagnostic	Read
B11y.00	Malignant neoplasm of other specified site of stomach	res14: Upper gastrointestinal malignancy	diagnostic	Read
B11y000	Malignant neoplasm of anterior wall of stomach NEC	res14: Upper gastrointestinal malignancy	diagnostic	Read
B11y100	Malignant neoplasm of posterior wall of stomach NEC	res14: Upper gastrointestinal malignancy	diagnostic	Read
B11yz00	Malignant neoplasm of other specified site of stomach NOS	res14: Upper gastrointestinal malignancy	diagnostic	Read
B11z.00	Malignant neoplasm of stomach NOS	res14: Upper gastrointestinal malignancy	diagnostic	Read
BB55.00	[M]Linitisplastica	res14: Upper gastrointestinal malignancy	diagnostic	Read
BB5C.00	[M]Gastrinoma and carcinomas	res14: Upper gastrointestinal malignancy	diagnostic	Read
BB5C000	[M]Gastrinoma NOS	res14: Upper gastrointestinal malignancy	diagnostic	Read
BB5C011	[M]G cell tumour NOS	res14: Upper gastrointestinal malignancy	diagnostic	Read
BB5C100	[M]Gastrinoma; malignant	res14: Upper gastrointestinal malignancy	diagnostic	Read
BB5Cz00	[M]Gastrinoma or carcinoma NOS	res14: Upper gastrointestinal malignancy	diagnostic	Read

API

To Export Phenotype Details:

Format	API
XML	site_root/api/v1/public/phenotypes/PH719/version/1438/detail/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH719/version/1438/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('PH719', '1438', api_client=client)`

To Export Phenotype Code List:

Format	API
XML	site_root/api/v1/public/phenotypes/PH719/version/1438/export/codes/?format=xml
JSON	site_root/api/v1/public/phenotypes/PH719/version/1438/export/codes/?format=json
CSV	site_root/phenotypes/PH719/version/1438/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('PH719', '1438', api_client=client)`

Version History

Version ID	Name	Owner	Publish date
1438	Upper Gastro Intestinal Malignancy	ieuan.scanlon	2021-10-06	currently shown