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Cancer Comorbidities

Romi Haas, Ljoudmila Busija, Alexandra Gorelik, Denise A O'Connor, Christopher Pierce, Danielle Mazza, Rochelle Buchbinder

ID
PH839
Version ID
1757
Type
Disease or Syndrome
Data Sources
POpulation Level Analysis and Reporting (POLAR) Database Australia
Valid event data range
01/01/2014 - 31/12/2018
Sex
♀  Female ♂  Male
Agreement Date
2021-09-24
Coding system
SNOMED CT codes
Collections
ClinicalCodes Repository Phenotype Library
Tags
No tags

Definition

Introduction:

General practice is integral to the Australian healthcare system. Outcome Health’s POpulation Level Analysis and Reporting (POLAR) database uses de-identified electronic health records to analyse general practice data in Australia. Previous studies using routinely collected health data for research have not consistently reported the codes and algorithms used to describe the population, exposures, interventions and outcomes in sufficient detail to allow replication. This paper reports a study protocol investigating patterns of care for people presenting with musculoskeletal conditions to general practice in Victoria, Australia. Its focus is on the systematic approach used to classify and select eligible records from the POLAR database to facilitate replication. This will be useful for other researchers using routinely collected health data for research.

Methods and analysis:

This is a retrospective cohort study. Patient-related data will be obtained through electronic health records from a subset of general practices across three primary health networks (PHN) in southeastern Victoria. Data for patients with a low back, neck, shoulder and/or knee condition and who received at least one general practitioner (GP) face-to-face consultation between 1 January 2014 and 31 December 2018 will be included. Data quality checks will be conducted to exclude patients with poor data recording and/or non-continuous follow-up. Relational data files with eligible and valid records will be merged to select the study cohort and the GP care received (consultations, imaging requests, prescriptions and referrals) between diagnosis and 31 December 2018. Number and characteristics of patients and GPs, and number, type and timing of imaging requests, prescriptions for pain relief and referrals to other health providers will be investigated.

Ethics and dissemination:

Ethics approval was obtained from the Cabrini and Monash University Human Research Ethics Committees (Reference Numbers 02-21-01-19 and 16975, respectively). Study findings will be reported to Outcome Health, participating PHNs, disseminated in academic journals and presented in conferences.

Publications

  • Romi Haas, Ljoudmila Busija, Alexandra Gorelik, Denise A O'Connor, Christopher Pierce, Danielle Mazza, Rochelle Buchbinder, Patterns of care for people presenting to Australian general practice with musculoskeletal complaints based on routinely collected data: protocol for an observational cohort study using the Population Level Analysis and Reporting (POLAR) database. BMJ Open, 11(e055528), 2021.

Clinical Code List

Rows: 186
Code Description Entity type Coding System (SNOMED) Category
10438002 Glomus tumour res174: cancer comorbidities SNOMED diagnostic
109385007 Kaposi's sarcoma (clinical) res174: cancer comorbidities SNOMED diagnostic
109978004 T-cell lymphoma (clinical) res174: cancer comorbidities SNOMED diagnostic
109979007 B cell lymphoma res174: cancer comorbidities SNOMED diagnostic
109995007 Myelodysplastic syndrome (clinical) res174: cancer comorbidities SNOMED diagnostic
115239009 Bone tumour res174: cancer comorbidities SNOMED diagnostic
11671000 Adenoid cystic carcinoma res174: cancer comorbidities SNOMED diagnostic
118600007 Malignant lymphoma (clinical) res174: cancer comorbidities SNOMED diagnostic
118601006 Non-Hodgkin's lymphoma (clinical) res174: cancer comorbidities SNOMED diagnostic
118613001 Hairy cell leukaemia (clinical) res174: cancer comorbidities SNOMED diagnostic
118617000 Burkitt's lymphoma (clinical) res174: cancer comorbidities SNOMED diagnostic
123841004 Neoplasm of uterine cervix res174: cancer comorbidities SNOMED diagnostic
123843001 Neoplasm of ovary res174: cancer comorbidities SNOMED diagnostic
123845008 Adenocarcinoma of endometrium res174: cancer comorbidities SNOMED diagnostic
126488004 Neoplasm of skin res174: cancer comorbidities SNOMED diagnostic
126713003 Neoplasm of lung res174: cancer comorbidities SNOMED diagnostic
126824007 Neoplasm of stomach res174: cancer comorbidities SNOMED diagnostic
126838000 Neoplasm of colon res174: cancer comorbidities SNOMED diagnostic
126851005 Neoplasm of liver res174: cancer comorbidities SNOMED diagnostic
126880001 Neoplasm of kidney res174: cancer comorbidities SNOMED diagnostic
126885006 Neoplasm of bladder res174: cancer comorbidities SNOMED diagnostic
126921000 Neoplasm of vagina res174: cancer comorbidities SNOMED diagnostic
126926005 Neoplasm of breast res174: cancer comorbidities SNOMED diagnostic
126949007 Acoustic neuroma res174: cancer comorbidities SNOMED diagnostic
126951006 Neoplasm of central nervous system res174: cancer comorbidities SNOMED diagnostic
126962006 Neoplasm of spinal cord res174: cancer comorbidities SNOMED diagnostic
127018007 Neoplasm of thyroid gland res174: cancer comorbidities SNOMED diagnostic
127020005 Neoplasm of parathyroid gland res174: cancer comorbidities SNOMED diagnostic
127021009 Neoplasm of adrenal gland res174: cancer comorbidities SNOMED diagnostic
127024001 Neoplasm of pituitary gland res174: cancer comorbidities SNOMED diagnostic
127225006 Chronic myelomonocytic leukaemia res174: cancer comorbidities SNOMED diagnostic
127231009 Neoplasm of thymus res174: cancer comorbidities SNOMED diagnostic
128462008 Secondary malignant neoplastic disease res174: cancer comorbidities SNOMED diagnostic
128474007 Parathyroid adenoma res174: cancer comorbidities SNOMED diagnostic
128822004 Precursor cell lymphoblastic leukaemia res174: cancer comorbidities SNOMED diagnostic
128929007 Non-Hodgkin lymphoma - category res174: cancer comorbidities SNOMED diagnostic
129000002 Langerhans cell histiocytosis, unifocal (clinical) res174: cancer comorbidities SNOMED diagnostic
14537002 Hodgkin lymphoma res174: cancer comorbidities SNOMED diagnostic
1651000119109 Primary adenocarcinoma of pancreas res174: cancer comorbidities SNOMED diagnostic
16652001 Fabry's disease res174: cancer comorbidities SNOMED diagnostic
1761000119103 Chronic obstructive airway disease with asthma res174: cancer comorbidities SNOMED diagnostic
188192002 Malignant neoplasm of endometrium of corpus uteri res174: cancer comorbidities SNOMED diagnostic
189336000 Carcinoma in situ of breast res174: cancer comorbidities SNOMED diagnostic
233854003 Atrial myxoma res174: cancer comorbidities SNOMED diagnostic
253010003 Microprolactinoma res174: cancer comorbidities SNOMED diagnostic
25370001 Hepatocellular carcinoma res174: cancer comorbidities SNOMED diagnostic
254582000 Adenocarcinoma of rectum res174: cancer comorbidities SNOMED diagnostic
254609000 Carcinoma of ampulla of Vater res174: cancer comorbidities SNOMED diagnostic
254622008 Squamous cell carcinoma of bronchus res174: cancer comorbidities SNOMED diagnostic
254626006 Adenocarcinoma of lung res174: cancer comorbidities SNOMED diagnostic
254629004 Large cell carcinoma of lung res174: cancer comorbidities SNOMED diagnostic
254632001 Small cell carcinoma of lung res174: cancer comorbidities SNOMED diagnostic
254634000 Squamous cell carcinoma of lung res174: cancer comorbidities SNOMED diagnostic
254637007 Non-small cell lung cancer res174: cancer comorbidities SNOMED diagnostic
254837009 Malignant tumour of breast res174: cancer comorbidities SNOMED diagnostic
254838004 Carcinoma of breast res174: cancer comorbidities SNOMED diagnostic
254849005 Malignant epithelial tumour of ovary res174: cancer comorbidities SNOMED diagnostic
254877001 Sarcoma of uterus res174: cancer comorbidities SNOMED diagnostic
25487800 Endometrial carcinoma res174: cancer comorbidities SNOMED diagnostic
254887002 Adenocarcinoma of cervix res174: cancer comorbidities SNOMED diagnostic
254893005 Carcinoma of vagina res174: cancer comorbidities SNOMED diagnostic
254900004 Carcinoma of prostate res174: cancer comorbidities SNOMED diagnostic
254915003 Clear cell carcinoma of kidney res174: cancer comorbidities SNOMED diagnostic
254935002 Intracranial tumour res174: cancer comorbidities SNOMED diagnostic
254956000 Pituitary adenoma res174: cancer comorbidities SNOMED diagnostic
254963000 Pituitary microadenoma res174: cancer comorbidities SNOMED diagnostic
254965007 Pituitary macroadenoma res174: cancer comorbidities SNOMED diagnostic
255029007 Papillary thyroid carcinoma res174: cancer comorbidities SNOMED diagnostic
255034006 Thyroid follicular adenoma res174: cancer comorbidities SNOMED diagnostic
255035007 Adrenal carcinoma res174: cancer comorbidities SNOMED diagnostic
255046005 Neuroendocrine tumour res174: cancer comorbidities SNOMED diagnostic
255081007 Carcinoma of caecum res174: cancer comorbidities SNOMED diagnostic
255084004 Squamous cell carcinoma of anal margin res174: cancer comorbidities SNOMED diagnostic
255108000 Carcinoma of bladder res174: cancer comorbidities SNOMED diagnostic
255109008 Transitional cell carcinoma of bladder res174: cancer comorbidities SNOMED diagnostic
269533000 Carcinoma of colon res174: cancer comorbidities SNOMED diagnostic
27090000 Transitional cell carcinoma res174: cancer comorbidities SNOMED diagnostic
276811008 Gastric lymphoma res174: cancer comorbidities SNOMED diagnostic
276975007 Carcinoma of larynx res174: cancer comorbidities SNOMED diagnostic
277637000 Large cell anaplastic lymphoma res174: cancer comorbidities SNOMED diagnostic
28054005 Cutaneous T-cell lymphoma res174: cancer comorbidities SNOMED diagnostic
285312008 Carcinoma of sigmoid colon res174: cancer comorbidities SNOMED diagnostic
285432005 Carcinoma of cervix res174: cancer comorbidities SNOMED diagnostic
301756000 Adenocarcinoma of sigmoid colon res174: cancer comorbidities SNOMED diagnostic
302822000 Insulinoma res174: cancer comorbidities SNOMED diagnostic
302823005 Glucagonoma res174: cancer comorbidities SNOMED diagnostic
302828001 Syringoma res174: cancer comorbidities SNOMED diagnostic
302841002 Malignant lymphoma - small lymphocytic res174: cancer comorbidities SNOMED diagnostic
302849000 Nephroblastoma res174: cancer comorbidities SNOMED diagnostic
309245001 Adenocarcinoma of uterus res174: cancer comorbidities SNOMED diagnostic
310498001 Malignant melanoma of back res174: cancer comorbidities SNOMED diagnostic
312823001 Villous adenoma of rectum res174: cancer comorbidities SNOMED diagnostic
315058005 Hereditary nonpolyposis colon cancer res174: cancer comorbidities SNOMED diagnostic
35868009 Carcinoid syndrome res174: cancer comorbidities SNOMED diagnostic
359987004 Krukenberg tumour res174: cancer comorbidities SNOMED diagnostic
363346000 Malignant neoplastic disease res174: cancer comorbidities SNOMED diagnostic
363349007 Malignant tumour of stomach res174: cancer comorbidities SNOMED diagnostic
363351006 Malignant tumour of rectum res174: cancer comorbidities SNOMED diagnostic
363358000 Malignant tumour of lung res174: cancer comorbidities SNOMED diagnostic
363402007 Malignant tumour of oesophagus res174: cancer comorbidities SNOMED diagnostic
363403002 Malignant tumour of duodenum res174: cancer comorbidities SNOMED diagnostic
363406005 Malignant tumour of colon res174: cancer comorbidities SNOMED diagnostic
363418001 Malignant tumour of pancreas res174: cancer comorbidities SNOMED diagnostic
363429002 Malignant tumour of larynx res174: cancer comorbidities SNOMED diagnostic
363443007 Malignant tumor of ovary res174: cancer comorbidities SNOMED diagnostic
363449006 Malignant tumor of testis res174: cancer comorbidities SNOMED diagnostic
363478007 Malignant tumour of thyroid gland res174: cancer comorbidities SNOMED diagnostic
363492001 Malignant tumour of peritoneum res174: cancer comorbidities SNOMED diagnostic
363507003 Malignant tumour of pharynx res174: cancer comorbidities SNOMED diagnostic
363508008 Malignant tumour of intestine res174: cancer comorbidities SNOMED diagnostic
363518003 Malignant tumour of kidney res174: cancer comorbidities SNOMED diagnostic
369766003 Low grade res174: cancer comorbidities SNOMED diagnostic
369850009 T1b: Tumour involves both vocal cords res174: cancer comorbidities SNOMED diagnostic
371486001 Neoplasm of eye proper res174: cancer comorbidities SNOMED diagnostic
372140005 Carcinoma of gallbladder res174: cancer comorbidities SNOMED diagnostic
372142002 Carcinoma of pancreas res174: cancer comorbidities SNOMED diagnostic
372143007 Carcinoma of stomach res174: cancer comorbidities SNOMED diagnostic
386792000 Transurethral resection of bladder neoplasm res174: cancer comorbidities SNOMED diagnostic
393563007 Glioblastoma multiforme res174: cancer comorbidities SNOMED diagnostic
393564001 Glioma res174: cancer comorbidities SNOMED diagnostic
399068003 Malignant tumour of prostate res174: cancer comorbidities SNOMED diagnostic
399326009 Malignant tumour of urinary bladder res174: cancer comorbidities SNOMED diagnostic
399490008 Adenocarcinoma of prostate res174: cancer comorbidities SNOMED diagnostic
400122007 Primary cutaneous T-cell lymphoma res174: cancer comorbidities SNOMED diagnostic
403202002 Multiple actinic keratoses res174: cancer comorbidities SNOMED diagnostic
403946000 Paget's disease of nipple res174: cancer comorbidities SNOMED diagnostic
404062002 Multiple lipomata res174: cancer comorbidities SNOMED diagnostic
408647009 Adenocarcinoma of stomach res174: cancer comorbidities SNOMED diagnostic
410812005 Dupuytren's disease res174: cancer comorbidities SNOMED diagnostic
413440007 Acute lymphoblastic leukaemia - category res174: cancer comorbidities SNOMED diagnostic
413839001 Chronic lung disease res174: cancer comorbidities SNOMED diagnostic
414629003 Lymphoproliferative disorder res174: cancer comorbidities SNOMED diagnostic
41607009 Renal cell carcinoma res174: cancer comorbidities SNOMED diagnostic
417570003 Gestational choriocarcinoma res174: cancer comorbidities SNOMED diagnostic
423673009 Malignant melanoma of retina res174: cancer comorbidities SNOMED diagnostic
428905002 Malignant neoplasm of gastrointestinal tract res174: cancer comorbidities SNOMED diagnostic
443250000 Malignant fibromatous neoplasm res174: cancer comorbidities SNOMED diagnostic
443333004 Medulloblastoma res174: cancer comorbidities SNOMED diagnostic
443439001 Malignant fibrous histiocytoma res174: cancer comorbidities SNOMED diagnostic
443487006 Mantle cell lymphoma res174: cancer comorbidities SNOMED diagnostic
443492008 Carcinoid tumour res174: cancer comorbidities SNOMED diagnostic
443493003 Metastatic malignant melanoma res174: cancer comorbidities SNOMED diagnostic
443520009 Chondrosarcoma res174: cancer comorbidities SNOMED diagnostic
443675005 Seminoma res174: cancer comorbidities SNOMED diagnostic
443719001 Leiomyosarcoma res174: cancer comorbidities SNOMED diagnostic
443936004 Oligodendroglioma res174: cancer comorbidities SNOMED diagnostic
443961001 Malignant adenomatous neoplasm res174: cancer comorbidities SNOMED diagnostic
445738007 Myelodysplastic/myeloproliferative disease res174: cancer comorbidities SNOMED diagnostic
446022000 Carcinoma of uterus res174: cancer comorbidities SNOMED diagnostic
447882007 Carcinoma of vulva res174: cancer comorbidities SNOMED diagnostic
447949005 Carcinoma of cheek res174: cancer comorbidities SNOMED diagnostic
448216007 Carcinoma of thyroid res174: cancer comorbidities SNOMED diagnostic
448930008 Squamous cell carcinoma of nose res174: cancer comorbidities SNOMED diagnostic
448989001 Carcinoma of brain res174: cancer comorbidities SNOMED diagnostic
448993007 Carcinoma of lung res174: cancer comorbidities SNOMED diagnostic
449248000 Nasopharyngeal carcinoma res174: cancer comorbidities SNOMED diagnostic
46732000 Malignant lymphoma, large B-cell, diffuse res174: cancer comorbidities SNOMED diagnostic
5052009 Merkel cell carcinoma res174: cancer comorbidities SNOMED diagnostic
51092000 Chronic lymphocytic leukaemia res174: cancer comorbidities SNOMED diagnostic
55150002 Follicular lymphoma res174: cancer comorbidities SNOMED diagnostic
55342001 Neoplastic disease res174: cancer comorbidities SNOMED diagnostic
62064005 Mesothelioma, malignant res174: cancer comorbidities SNOMED diagnostic
65399007 Langerhans cell histiocytosis res174: cancer comorbidities SNOMED diagnostic
65692009 spindle cell carcinoma res174: cancer comorbidities SNOMED diagnostic
68453008 Carcinoma res174: cancer comorbidities SNOMED diagnostic
77284006 Lobular carcinoma in situ res174: cancer comorbidities SNOMED diagnostic
79282002 Carcinoma metastatic res174: cancer comorbidities SNOMED diagnostic
82711006 Infiltrating duct carcinoma res174: cancer comorbidities SNOMED diagnostic
83270006 Neoplastic pleural effusion res174: cancer comorbidities SNOMED diagnostic
86049000 Neoplasm, malignant (primary) res174: cancer comorbidities SNOMED diagnostic
86616005 Intraductal carcinoma, noninfiltrating res174: cancer comorbidities SNOMED diagnostic
91855006 Acute leukaemia res174: cancer comorbidities SNOMED diagnostic
91857003 Acute lymphoid leukaemia res174: cancer comorbidities SNOMED diagnostic
91861009 Acute myeloid leukaemia disease res174: cancer comorbidities SNOMED diagnostic
92814006 Chronic lymphoid leukaemia, disease res174: cancer comorbidities SNOMED diagnostic
92818009 Chronic myeloid leukaemia res174: cancer comorbidities SNOMED diagnostic
93143009 Leukemia res174: cancer comorbidities SNOMED diagnostic
93781006 Primary malignant neoplasm of endometrium res174: cancer comorbidities SNOMED diagnostic
93870000 Malignant neoplasm of liver res174: cancer comorbidities SNOMED diagnostic
94006002 Primary malignant neoplasm of sigmoid colon res174: cancer comorbidities SNOMED diagnostic
94222008 Secondary malignant neoplasm of bone res174: cancer comorbidities SNOMED diagnostic
94225005 Secondary malignant neoplasm of brain res174: cancer comorbidities SNOMED diagnostic
94245002 Secondary malignant neoplasm of cerebellum res174: cancer comorbidities SNOMED diagnostic
94248000 Secondary malignant neoplasm of cerebrum res174: cancer comorbidities SNOMED diagnostic
94381002 Secondary malignant neoplasm of liver res174: cancer comorbidities SNOMED diagnostic
94391008 Secondary malignant neoplasm of lung res174: cancer comorbidities SNOMED diagnostic

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH839/version/1757/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH839/version/1757/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('PH839', '1757', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH839/version/1757/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH839/version/1757/export/codes/?format=json
CSV site_root/phenotypes/PH839/version/1757/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('PH839', '1757', api_client=client)

Version History

Version
ID
Name Owner Publish date
1757 Cancer Comorbidities ieuan.scanlon 2022-04-04 currently shown

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