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Chronic Kidney Disease

Evangelos Kontopantelis, David A Springate, David Reeves, Darren M. Aschroff, Martin Rutter, Iain Buchan, Tim Doran, Matthias Pierce, Darren M. Ashcroft

Type
Disease or Syndrome
ID
PH509
Version ID
1018
Data Sources
Valid event data range
01/04/2006 - 31/03/2012
Sex
Female, Male
Agreement Date
2014-12-16
Coding system
Read codes v2
Tags /Collections
ClinicalCodes Repository Phenotype Library

Definition

Data source:

We used the Clinical Practice Research Datalink (CPRD), a large primary care database that holds complete electronic patient records (including diagnoses, prescriptions and referrals) from participating family practices across the UK. A hierarchical clinical coding system (Read) is used to record the data. In July 2012, data were available for 644 practices and 13,772,992 patients. Full details of the database have been provided elsewhere.

Diabetes cohort:

We extracted data from 1 April 2006 to 31 March 2012 and, for ease of reporting and analysing, aggregated information into six financial years. Within each year, practice inclusion eligibility was determined by a CPRD assessment algorithm, which informs on practices considered to be of research standard; therefore, our cohort of practices varied over time. For each research standard practice and year, we defined as eligible patients those who were registered with the practice for the full year and were aged 18 years or over in that year. From these patients, using relevant Read codes for type 2 diabetes (e.g. C10F.00: Type 2 diabetes mellitus) and excluding those treated with insulin within 2 years of diagnosis, we identified 246,544 patients over the study period. Diagnoses were not constrained to the study period and a relevant code prior to the study as well as during the study period would flag a patient from the respective year onwards. Data on sex, age and removal from the database due to deaths were available and complete for all patients.We extracted data on diabetes-related macrovascular (myocardial infarction, stroke, peripheral vascular disease or amputation) and microvascular (retinopathy, neuropathy, nephropathy [chronic kidney disease stages 4–5] or foot ulcer) complications as well as comorbidities (asthma, coronary heart disease, chronic kidney disease [excluded from microvascular analysis], chronic obstructive pulmonary disease, depression, dementia, severe mental illness, heart failure, hypertension, stroke [excluded from macrovascular analysis], cancer, epilepsy, osteoarthritis, osteoporosis and hypothyroidism). Although we aimed to include all conditions associated with diabetes, the choice was partially determined by the domains incentivised under the Quality and Outcomes Framework (QOF), for which accuracy of diagnosis is considered high. Information was also extracted on smoking (never smoked, current, exsmoker and missing data),BMI, HbA1c levels (%), cholesterol levels (mmol/l) and systolic/diastolic BP (mmHg). Biometric measurement data were cleaned and we calculated patient means for each year when more than one relevant record was available. Using product lists we determined prescription prevalence (at least one) for relevant medications: ACE inhibitors, acarbose, α-blockers, anticoagulants, antiplatelet agents, β-blockers, calcium-channel blockers, thiazide diuretics, loop diuretics, dipeptidyl peptidase-4 inhibitors, glucagon-like peptide- 1 agonists, statins and other lipid-lowering drugs, meglitinides , metformin, sulfonylureas and thiazolidinediones. For approximately 60% of the practices, records were linked to Office of National Statistics (ONS) mortality data and we had access to death dates for all their patients. For these, using ICD-10 codes (www.who.int/classifications/icd/en/) we were able to estimate deathslinked to specific causes (underlying or in the top three): diabetes (E10–E16), ischaemic heart disease (I21–I22), stroke (I60–I64) or stroke excluding bleeds (excluding I63).

Publications

  • Evangelos Kontopantelis, David A Springate, David Reeves, Darren M. Aschroff, Martin Rutter, Iain Buchan, Tim Doran, Glucose, blood pressure and cholesterol levels and their relationships to clinical outcomes in type 2 diabetes: a retrospective cohort study. Diabetologia, 58:505-518, 2015.

Clinical Code List

Rows: 74
Code Description Entity type Category Coding System (Read)
10081 Chronic uraemia Chronic Kidney Disease diagnostic Read
10647 Nephritis - chronic Chronic Kidney Disease diagnostic Read
10809 Chronic membranous glomerulonephritis Chronic Kidney Disease diagnostic Read
11553 Kidney transplant failure and rejection Chronic Kidney Disease diagnostic Read
11875 Nephropathy - chronic Chronic Kidney Disease diagnostic Read
12479 Chronic kidney disease stage 4 Chronic Kidney Disease diagnostic Read
12566 Chronic kidney disease stage 3 Chronic Kidney Disease diagnostic Read
12585 Chronic kidney disease stage 5 Chronic Kidney Disease diagnostic Read
15097 Chronic glomerulonephritis NOS Chronic Kidney Disease diagnostic Read
17253 Renal transplant planned Chronic Kidney Disease diagnostic Read
17365 Nephrotic syndrome; diffuse crescentic glomerulonephritis Chronic Kidney Disease diagnostic Read
1803 Nephrotic syndrome with membranous glomerulonephritis Chronic Kidney Disease diagnostic Read
18774 Renal transplant with complication; without blame Chronic Kidney Disease diagnostic Read
19316 Nephrotic syndrome; diffuse membranous glomerulonephritis Chronic Kidney Disease diagnostic Read
21158 Chronic pyelitis Chronic Kidney Disease diagnostic Read
21947 Nephrotic syn difus mesangial prolifertiv glomerulonephritis Chronic Kidney Disease diagnostic Read
21989 Nephrotic syn;diffuse mesangiocapillary glomerulonephritis Chronic Kidney Disease diagnostic Read
22205 Lupus nephritis Chronic Kidney Disease diagnostic Read
22852 Nephrotic syndrome; focal and segmental glomerular lesions Chronic Kidney Disease diagnostic Read
23913 Nephrotic syndrome; minor glomerular abnormality Chronic Kidney Disease diagnostic Read
2471 Nephrotic syndrome in diabetes mellitus Chronic Kidney Disease diagnostic Read
25055 Chronic pyonephrosis Chronic Kidney Disease diagnostic Read
26862 Exploration of renal transplant Chronic Kidney Disease diagnostic Read
27427 Nephrotic syndrome NOS Chronic Kidney Disease diagnostic Read
2939 Calculous pyelonephritis Chronic Kidney Disease diagnostic Read
29634 Nephrotic syndrome with minimal change glomerulonephritis Chronic Kidney Disease diagnostic Read
2999 Nephrotic syndrome Chronic Kidney Disease diagnostic Read
34998 Chronic proliferative glomerulonephritis Chronic Kidney Disease diagnostic Read
35360 Nonobstructive reflux-associated chronic pyelonephritis Chronic Kidney Disease diagnostic Read
40349 Lipoid nephrosis Chronic Kidney Disease diagnostic Read
45499 Kimmelstiel - Wilson disease Chronic Kidney Disease diagnostic Read
4654 Chronic pyelonephritis Chronic Kidney Disease diagnostic Read
4669 Chronic focal glomerulonephritis Chronic Kidney Disease diagnostic Read
47672 Nephrotic syndrome in systemic lupus erythematosus Chronic Kidney Disease diagnostic Read
47922 Nephrotic syndrome in amyloidosis Chronic Kidney Disease diagnostic Read
48111 Chronic pyelonephritis NOS Chronic Kidney Disease diagnostic Read
48855 Chronic obstructive pyelonephritis Chronic Kidney Disease diagnostic Read
50472 Nephrotic syn;difus endocapilary proliftv glomerulonephritis Chronic Kidney Disease diagnostic Read
512 Chronic renal failure Chronic Kidney Disease diagnostic Read
53852 End stage renal failure Chronic Kidney Disease diagnostic Read
54990 Kidney transplant with complication; without blame Chronic Kidney Disease diagnostic Read
56987 Nephrotic syndrome; dense deposit disease Chronic Kidney Disease diagnostic Read
57568 Chronic pyelonephritis with medullary necrosis Chronic Kidney Disease diagnostic Read
57926 Steroid sensitive nephrotic syndrome Chronic Kidney Disease diagnostic Read
58750 Nephrotic syndrome in polyarteritis nodosa Chronic Kidney Disease diagnostic Read
5911 [V]Kidney transplanted Chronic Kidney Disease diagnostic Read
60960 Other chronic glomerulonephritis Chronic Kidney Disease diagnostic Read
61494 Chronic membranoproliferative glomerulonephritis Chronic Kidney Disease diagnostic Read
63615 Other chronic glomerulonephritis NOS Chronic Kidney Disease diagnostic Read
63786 Congenital nephrotic syndrome Chronic Kidney Disease diagnostic Read
65064 Chronic rapidly progressive glomerulonephritis Chronic Kidney Disease diagnostic Read
65400 Chronic diffuse glomerulonephritis Chronic Kidney Disease diagnostic Read
6712 End stage renal failure Chronic Kidney Disease diagnostic Read
72303 Finnish nephrosis syndrome Chronic Kidney Disease diagnostic Read
7804 Chronic glomerulonephritis Chronic Kidney Disease diagnostic Read
8330 End-stage renal disease Chronic Kidney Disease diagnostic Read
94373 Nephrotic syndrome with other pathological kidney lesions Chronic Kidney Disease diagnostic Read
94793 Chronic kidney disease stage 3 with proteinuria Chronic Kidney Disease diagnostic Read
94965 Chronic kidney disease stage 3A Chronic Kidney Disease diagnostic Read
95122 Chronic kidney disease stage 4 with proteinuria Chronic Kidney Disease diagnostic Read
95123 Chronic kidney disease stage 3 without proteinuria Chronic Kidney Disease diagnostic Read
95175 Chronic kidney disease stage 3A without proteinuria Chronic Kidney Disease diagnostic Read
95177 Chronic kidney disease stage 3B without proteinuria Chronic Kidney Disease diagnostic Read
95178 Chronic kidney disease stage 3B with proteinuria Chronic Kidney Disease diagnostic Read
95179 Chronic kidney disease stage 3B Chronic Kidney Disease diagnostic Read
95405 Chronic kidney disease stage 5 without proteinuria Chronic Kidney Disease diagnostic Read
95406 Chronic kidney disease stage 4 without proteinuria Chronic Kidney Disease diagnostic Read
95408 Chronic kidney disease stage 3A with proteinuria Chronic Kidney Disease diagnostic Read
95508 Chronic kidney disease stage 5 with proteinuria Chronic Kidney Disease diagnostic Read
97758 Chronic glomerulonephritis + diseases EC Chronic Kidney Disease diagnostic Read
9840 Nephrotic syndrome with proliferative glomerulonephritis Chronic Kidney Disease diagnostic Read
99201 Nephrotic syndrome in malaria Chronic Kidney Disease diagnostic Read
99631 Chronic pyelonephritis without medullary necrosis Chronic Kidney Disease diagnostic Read
99644 Nephrotic syndrome+membranoproliferative glomerulonephritis Chronic Kidney Disease diagnostic Read

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH509/version/1018/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH509/version/1018/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('PH509', '1018', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH509/version/1018/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH509/version/1018/export/codes/?format=json
CSV site_root/phenotypes/PH509/version/1018/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('PH509', '1018', api_client=client)

Version History

Version
ID
Name Owner Publish date
1018 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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