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Rheumatoid Arthritis

Evangelos Kontopantelis, Ivan Olier, Claire Planner, David Reeves, Darren M Ashcroft, Linda Gask, Tim Doran, Sioban Reilly

Type
Disease or Syndrome
ID
PH555
Version ID
1110
Data Sources
Valid event data range
01/04/2000 - 31/03/2012
Sex
Female, Male
Agreement Date
2015-12-16
Coding system
Read codes v2
Tags /Collections
ClinicalCodes Repository Phenotype Library

Definition

The database:

The CPRD is a large computerised database of anonymised primary care medical records. It contains complete patient information for participating practices, with the healthcare events (diagnoses, treatments, referrals, tests and prescriptions) recorded using coding systems (Read coding for diagnoses). Practice characteristics are described in detail elsewhere. The database is broadly representative of the UK population, although larger practices are over-represented. Practices need to meet prespecified data entry quality criteria to be defined as ‘up to research standard’, and for each study year, our main sample included all CPRD practices that were classed as such for the whole year. We also generated two data sets to test the sensitivity of our findings. First, we included all practices contributing data across the entire study period. Second, we included a subsample of 50 practices, representative of UK practices in terms of area deprivation, and practice list size.

Defining people with SMI and controls:

Information was extracted for the period 1 April 2000 to 31 March 2012 and aggregated into 12 yearly ‘bins’, to correspond with financial years 2000/2001–2011/2012. We used Read codes to identify the presence of SMI. First, we identified relevant keywords (or key-stubs) and codes, for example ‘paranoi’ and ‘E100.00’ (simple schizophrenia). Next, the CPRD was searched for codes that matched the list in either the code or the description field. Finally, the matched code list was reviewed by clinical experts and a final conservative list of codes was agreed. A similar process was used to define comorbidities (hypertension, asthma, hypothyroidism, osteoarthritis, chronic kidney disease, coronary heart disease, epilepsy, chronic obstructive pulmonary disease, cancer, stroke, heart failure, rheumatoid arthritis, dementia and psoriasis). All code lists we used are available from http://www.clinicalcodes.org. All conditions, bar asthma, were treated as unresolvable (ie, permanent). Within each year, all patients registered with a CPRD practice for the whole year and aged 18 or over were eligible for inclusion. The final SMI Read code list was used to identify cases of SMI, which were then grouped into three broad subcategories, in line with the diagnoses used when compiling primary care QOF SMI registers: schizophrenia; affective psychoses (bipolar disorder or other unspecified affective psychosis); other types of psychosis. In the event that an individual received more than one SMI diagnosis over the study period, we used the last available diagnosis to retrospectively ‘correct’ the original diagnosis (ie, we assumed that the latest diagnosis was the correct one). Within each year, each SMI case was then matched on age, sex and practice to five randomly selected patients not associated with SMI up until that time point. More details on the extraction of the cohort have been provided elsewhere,21 and a flow chart of the data extraction process is available in the online appendix figure A2.

Defining consultation type:

We defined a ‘consultation’ as involving direct contact between a patient and a healthcare professional within the primary care setting. We divided consultations into two main categories: face-to-face (our primary outcome), and by telephone (see online appendix table A1). We also constructed a third ‘other’ grouping of all other activities that are captured by the ‘consultation type’ codes within the CPRD. This includes mail/email contact, third party consultations (including referrals), secondary care episodes, other administrative tasks and consultations of unknown content. This group is highly heterogeneous and includes many activities that cannot be classed as consultations. However, we decided to use this grouping as an aggregate secondary outcome since it can potentially provide insight into the overall workload associated with patient care in the primary care context. We decided against breaking down the ‘other’ group in more subcategories as we are very doubtful regarding the reliability and across practice consistency of the coding within these ‘other’ categories. In instances where a patient had two or more consultations within a day, we conservatively assumed a single consultation took place, to reduce the likelihood of including duplicate records.

Publications

  • Evangelos Kontopantelis, Ivan Olier, Claire Panner, David Reeves, Darren M Ashcroft, Linda Gask, Tim Doran, Siobhan Reilly, Primary care consultation rates among people with and without severe mental illness a UK cohort study using the Clinical Practice Research Datalink. BMJ Open, 5 (e008650), 2015.

Clinical Code List

Rows: 54
Code Description Entity type Category Coding System (Read)
14G1.00 H/O: rheumatoid arthritis res21: RA diagnostic Read
38DZ.00 Disease activity score in rheumatoid arthritis res21: RA diagnostic Read
66H..13 Rheumatoid arthrit. monitoring res21: RA diagnostic Read
7P20300 Delivery of rehabilitation for rheumatoid arthritis res21: RA diagnostic Read
F371200 Polyneuropathy in rheumatoid arthritis res21: RA diagnostic Read
F396400 Myopathy due to rheumatoid arthritis res21: RA diagnostic Read
G5y8.00 Rheumatoid myocarditis res21: RA diagnostic Read
G5yA.00 Rheumatoid carditis res21: RA diagnostic Read
H570.00 Rheumatoid lung res21: RA diagnostic Read
N04..00 Rheumatoid arthritis and other inflammatory polyarthropathy res21: RA diagnostic Read
N040.00 Rheumatoid arthritis res21: RA diagnostic Read
N040000 Rheumatoid arthritis of cervical spine res21: RA diagnostic Read
N040100 Other rheumatoid arthritis of spine res21: RA diagnostic Read
N040200 Rheumatoid arthritis of shoulder res21: RA diagnostic Read
N040400 Rheumatoid arthritis of acromioclavicular joint res21: RA diagnostic Read
N040500 Rheumatoid arthritis of elbow res21: RA diagnostic Read
N040600 Rheumatoid arthritis of distal radio-ulnar joint res21: RA diagnostic Read
N040700 Rheumatoid arthritis of wrist res21: RA diagnostic Read
N040800 Rheumatoid arthritis of MCP joint res21: RA diagnostic Read
N040900 Rheumatoid arthritis of PIP joint of finger res21: RA diagnostic Read
N040A00 Rheumatoid arthritis of DIP joint of finger res21: RA diagnostic Read
N040B00 Rheumatoid arthritis of hip res21: RA diagnostic Read
N040C00 Rheumatoid arthritis of sacro-iliac joint res21: RA diagnostic Read
N040D00 Rheumatoid arthritis of knee res21: RA diagnostic Read
N040F00 Rheumatoid arthritis of ankle res21: RA diagnostic Read
N040G00 Rheumatoid arthritis of subtalar joint res21: RA diagnostic Read
N040H00 Rheumatoid arthritis of talonavicular joint res21: RA diagnostic Read
N040J00 Rheumatoid arthritis of other tarsal joint res21: RA diagnostic Read
N040K00 Rheumatoid arthritis of 1st MTP joint res21: RA diagnostic Read
N040L00 Rheumatoid arthritis of lesser MTP joint res21: RA diagnostic Read
N040N00 Rheumatoid vasculitis res21: RA diagnostic Read
N040P00 Seronegative rheumatoid arthritis res21: RA diagnostic Read
N040R00 Rheumatoid nodule res21: RA diagnostic Read
N040S00 Rheumatoid arthritis - multiple joint res21: RA diagnostic Read
N040T00 Flare of rheumatoid arthritis res21: RA diagnostic Read
N041.00 Felty's syndrome res21: RA diagnostic Read
N042.00 Other rheumatoid arthropathy + visceral/systemic involvement res21: RA diagnostic Read
N042100 Rheumatoid lung disease res21: RA diagnostic Read
N042200 Rheumatoid nodule res21: RA diagnostic Read
N042z00 Rheumatoid arthropathy + visceral/systemic involvement NOS res21: RA diagnostic Read
N043000 Juvenile rheumatoid arthropathy unspecified res21: RA diagnostic Read
N043100 Acute polyarticular juvenile rheumatoid arthritis res21: RA diagnostic Read
N043200 Pauciarticular juvenile rheumatoid arthritis res21: RA diagnostic Read
N043300 Monarticular juvenile rheumatoid arthritis res21: RA diagnostic Read
N043z00 Juvenile rheumatoid arthritis NOS res21: RA diagnostic Read
N045500 Juvenile rheumatoid arthritis res21: RA diagnostic Read
N047.00 Seropositive errosive rheumatoid arthritis res21: RA diagnostic Read
N04X.00 Seropositive rheumatoid arthritis, unspecified res21: RA diagnostic Read
N04y000 Rheumatoid lung res21: RA diagnostic Read
N04y011 Caplan's syndrome res21: RA diagnostic Read
N04y012 Fibrosing alveolitis associated with rheumatoid arthritis res21: RA diagnostic Read
Nyu1100 [X]Other seropositive rheumatoid arthritis res21: RA diagnostic Read
Nyu1200 [X]Other specified rheumatoid arthritis res21: RA diagnostic Read
Nyu1G00 [X]Seropositive rheumatoid arthritis, unspecified res21: RA diagnostic Read

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH555/version/1110/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH555/version/1110/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('PH555', '1110', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH555/version/1110/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH555/version/1110/export/codes/?format=json
CSV site_root/phenotypes/PH555/version/1110/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('PH555', '1110', api_client=client)

Version History

Version
ID
Name Owner Publish date
1110 Rheumatoid Arthritis 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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