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Chronic Kidney Disease

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

Type
Disease or Syndrome
ID
PH510
Version ID
1020
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: 74
Code Description Entity type Category Coding System (Read)
1Z12.00 Chronic kidney disease stage 3 res21: CKD diagnostic Read
1Z13.00 Chronic kidney disease stage 4 res21: CKD diagnostic Read
1Z14.00 Chronic kidney disease stage 5 res21: CKD diagnostic Read
1Z15.00 Chronic kidney disease stage 3A res21: CKD diagnostic Read
1Z16.00 Chronic kidney disease stage 3B res21: CKD diagnostic Read
1Z1B.00 Chronic kidney disease stage 3 with proteinuria res21: CKD diagnostic Read
1Z1C.00 Chronic kidney disease stage 3 without proteinuria res21: CKD diagnostic Read
1Z1D.00 Chronic kidney disease stage 3A with proteinuria res21: CKD diagnostic Read
1Z1E.00 Chronic kidney disease stage 3A without proteinuria res21: CKD diagnostic Read
1Z1F.00 Chronic kidney disease stage 3B with proteinuria res21: CKD diagnostic Read
1Z1G.00 Chronic kidney disease stage 3B without proteinuria res21: CKD diagnostic Read
1Z1H.00 Chronic kidney disease stage 4 with proteinuria res21: CKD diagnostic Read
1Z1J.00 Chronic kidney disease stage 4 without proteinuria res21: CKD diagnostic Read
1Z1K.00 Chronic kidney disease stage 5 with proteinuria res21: CKD diagnostic Read
1Z1L.00 Chronic kidney disease stage 5 without proteinuria res21: CKD diagnostic Read
7B06300 Exploration of renal transplant res21: CKD diagnostic Read
8L50.00 Renal transplant planned res21: CKD diagnostic Read
K01..00 Nephrotic syndrome res21: CKD diagnostic Read
K010.00 Nephrotic syndrome with proliferative glomerulonephritis res21: CKD diagnostic Read
K011.00 Nephrotic syndrome with membranous glomerulonephritis res21: CKD diagnostic Read
K012.00 Nephrotic syndrome+membranoproliferative glomerulonephritis res21: CKD diagnostic Read
K013.00 Nephrotic syndrome with minimal change glomerulonephritis res21: CKD diagnostic Read
K013.11 Lipoid nephrosis res21: CKD diagnostic Read
K013.12 Steroid sensitive nephrotic syndrome res21: CKD diagnostic Read
K014.00 Nephrotic syndrome, minor glomerular abnormality res21: CKD diagnostic Read
K015.00 Nephrotic syndrome, focal and segmental glomerular lesions res21: CKD diagnostic Read
K016.00 Nephrotic syndrome, diffuse membranous glomerulonephritis res21: CKD diagnostic Read
K017.00 Nephrotic syn difus mesangial prolifertiv glomerulonephritis res21: CKD diagnostic Read
K018.00 Nephrotic syn,difus endocapilary proliftv glomerulonephritis res21: CKD diagnostic Read
K019.00 Nephrotic syn,diffuse mesangiocapillary glomerulonephritis res21: CKD diagnostic Read
K01A.00 Nephrotic syndrome, dense deposit disease res21: CKD diagnostic Read
K01B.00 Nephrotic syndrome, diffuse crescentic glomerulonephritis res21: CKD diagnostic Read
K01w.00 Congenital nephrotic syndrome res21: CKD diagnostic Read
K01w000 Finnish nephrosis syndrome res21: CKD diagnostic Read
K01x000 Nephrotic syndrome in amyloidosis res21: CKD diagnostic Read
K01x100 Nephrotic syndrome in diabetes mellitus res21: CKD diagnostic Read
K01x111 Kimmelstiel - Wilson disease res21: CKD diagnostic Read
K01x200 Nephrotic syndrome in malaria res21: CKD diagnostic Read
K01x300 Nephrotic syndrome in polyarteritis nodosa res21: CKD diagnostic Read
K01x400 Nephrotic syndrome in systemic lupus erythematosus res21: CKD diagnostic Read
K01x411 Lupus nephritis res21: CKD diagnostic Read
K01y.00 Nephrotic syndrome with other pathological kidney lesions res21: CKD diagnostic Read
K01z.00 Nephrotic syndrome NOS res21: CKD diagnostic Read
K02..00 Chronic glomerulonephritis res21: CKD diagnostic Read
K02..11 Nephritis - chronic res21: CKD diagnostic Read
K02..12 Nephropathy - chronic res21: CKD diagnostic Read
K020.00 Chronic proliferative glomerulonephritis res21: CKD diagnostic Read
K021.00 Chronic membranous glomerulonephritis res21: CKD diagnostic Read
K022.00 Chronic membranoproliferative glomerulonephritis res21: CKD diagnostic Read
K023.00 Chronic rapidly progressive glomerulonephritis res21: CKD diagnostic Read
K02y.00 Other chronic glomerulonephritis res21: CKD diagnostic Read
K02y000 Chronic glomerulonephritis + diseases EC res21: CKD diagnostic Read
K02y200 Chronic focal glomerulonephritis res21: CKD diagnostic Read
K02y300 Chronic diffuse glomerulonephritis res21: CKD diagnostic Read
K02yz00 Other chronic glomerulonephritis NOS res21: CKD diagnostic Read
K02z.00 Chronic glomerulonephritis NOS res21: CKD diagnostic Read
K05..00 Chronic renal failure res21: CKD diagnostic Read
K05..11 Chronic uraemia res21: CKD diagnostic Read
K05..12 End stage renal failure res21: CKD diagnostic Read
K050.00 End stage renal failure res21: CKD diagnostic Read
K0D..00 End-stage renal disease res21: CKD diagnostic Read
K100.00 Chronic pyelonephritis res21: CKD diagnostic Read
K100000 Chronic pyelonephritis without medullary necrosis res21: CKD diagnostic Read
K100100 Chronic pyelonephritis with medullary necrosis res21: CKD diagnostic Read
K100200 Chronic pyelitis res21: CKD diagnostic Read
K100300 Chronic pyonephrosis res21: CKD diagnostic Read
K100400 Nonobstructive reflux-associated chronic pyelonephritis res21: CKD diagnostic Read
K100500 Chronic obstructive pyelonephritis res21: CKD diagnostic Read
K100600 Calculous pyelonephritis res21: CKD diagnostic Read
K100z00 Chronic pyelonephritis NOS res21: CKD diagnostic Read
SP08300 Kidney transplant failure and rejection res21: CKD diagnostic Read
TB00100 Kidney transplant with complication, without blame res21: CKD diagnostic Read
TB00111 Renal transplant with complication, without blame res21: CKD diagnostic Read
ZV42000 [V]Kidney transplanted res21: CKD diagnostic Read

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH510/version/1020/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH510/version/1020/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('PH510', '1020', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH510/version/1020/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH510/version/1020/export/codes/?format=json
CSV site_root/phenotypes/PH510/version/1020/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('PH510', '1020', api_client=client)

Version History

Version
ID
Name Owner Publish date
1020 Chronic Kidney Disease 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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