[ { "phenotype_id": "PH510", "phenotype_version_id": 1020, "name": "Chronic Kidney Disease", "definition": "The database:\n\nThe 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.\n\n\nDefining people with SMI and controls:\n\nInformation 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.\n\n\nDefining consultation type:\n\nWe 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.\n\n\n\n\n\n\n\n\n", "implementation": "", "publications": [ { "doi": null, "details": "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." } ], "validation": "", "citation_requirements": "", "created": "2021-10-06T16:23:07.767008Z", "author": "Evangelos Kontopantelis, Ivan Olier, Claire Planner, David Reeves, Darren M Ashcroft, Linda Gask, Tim Doran, Sioban Reilly", "collections": [ { "name": "ClinicalCodes Repository", "value": 25 }, { "name": "Phenotype Library", "value": 18 } ], "tags": null, "organisation": null, "world_access": 1, "updated": "2021-10-06T16:23:07.767036Z", "sex": [ { "name": "Both", "value": "3" } ], "type": [ { "name": "Disease or syndrome", "value": "2" } ], "ontology": null, "phenoflowid": "", "data_sources": [ { "name": "CPRD GOLD", "value": 5, "uid": "a29feafa-7bdd-44e9-b977-c9d26425e67f", "url": "https://healthdatagateway.org/en/dataset/694", "datasource_id": 694 } ], "coding_system": [ { "name": "Read codes v2", "value": 5 } ], "event_date_range": "01/04/2000 - 31/03/2012", "concept_information": [ { "concept_id": 1881, "concept_version_id": 4900, "concept_name": "Chronic Kidney Disease - Primary Care", "coding_system": { "id": 5, "name": "Read codes v2", "description": "Read codes v2" }, "phenotype_id": "PH510", "phenotype_version_id": 1020, "phenotype_name": "Chronic Kidney Disease", "code_attribute_header": [ "Entity type", "Category", "Coding System (Read)" ], "codes": [ { "code": "1Z12.00", "description": "Chronic kidney disease stage 3", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z13.00", "description": "Chronic kidney disease stage 4", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z14.00", "description": "Chronic kidney disease stage 5", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z15.00", "description": "Chronic kidney disease stage 3A", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z16.00", "description": "Chronic kidney disease stage 3B", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z1B.00", "description": "Chronic kidney disease stage 3 with proteinuria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z1C.00", "description": "Chronic kidney disease stage 3 without proteinuria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z1D.00", "description": "Chronic kidney disease stage 3A with proteinuria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z1E.00", "description": "Chronic kidney disease stage 3A without proteinuria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z1F.00", "description": "Chronic kidney disease stage 3B with proteinuria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z1G.00", "description": "Chronic kidney disease stage 3B without proteinuria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z1H.00", "description": "Chronic kidney disease stage 4 with proteinuria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z1J.00", "description": "Chronic kidney disease stage 4 without proteinuria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z1K.00", "description": "Chronic kidney disease stage 5 with proteinuria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "1Z1L.00", "description": "Chronic kidney disease stage 5 without proteinuria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "7B06300", "description": "Exploration of renal transplant", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "8L50.00", "description": "Renal transplant planned", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01..00", "description": "Nephrotic syndrome", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K010.00", "description": "Nephrotic syndrome with proliferative glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K011.00", "description": "Nephrotic syndrome with membranous glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K012.00", "description": "Nephrotic syndrome+membranoproliferative glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K013.00", "description": "Nephrotic syndrome with minimal change glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K013.11", "description": "Lipoid nephrosis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K013.12", "description": "Steroid sensitive nephrotic syndrome", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K014.00", "description": "Nephrotic syndrome, minor glomerular abnormality", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K015.00", "description": "Nephrotic syndrome, focal and segmental glomerular lesions", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K016.00", "description": "Nephrotic syndrome, diffuse membranous glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K017.00", "description": "Nephrotic syn difus mesangial prolifertiv glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K018.00", "description": "Nephrotic syn,difus endocapilary proliftv glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K019.00", "description": "Nephrotic syn,diffuse mesangiocapillary glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01A.00", "description": "Nephrotic syndrome, dense deposit disease", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01B.00", "description": "Nephrotic syndrome, diffuse crescentic glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01w.00", "description": "Congenital nephrotic syndrome", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01w000", "description": "Finnish nephrosis syndrome", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01x000", "description": "Nephrotic syndrome in amyloidosis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01x100", "description": "Nephrotic syndrome in diabetes mellitus", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01x111", "description": "Kimmelstiel - Wilson disease", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01x200", "description": "Nephrotic syndrome in malaria", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01x300", "description": "Nephrotic syndrome in polyarteritis nodosa", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01x400", "description": "Nephrotic syndrome in systemic lupus erythematosus", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01x411", "description": "Lupus nephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01y.00", "description": "Nephrotic syndrome with other pathological kidney lesions", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K01z.00", "description": "Nephrotic syndrome NOS", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K02..00", "description": "Chronic glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K020.00", "description": "Chronic proliferative glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K021.00", "description": "Chronic membranous glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K02..11", "description": "Nephritis - chronic", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K02..12", "description": "Nephropathy - chronic", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K022.00", "description": "Chronic membranoproliferative glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K023.00", "description": "Chronic rapidly progressive glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K02y.00", "description": "Other chronic glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K02y000", "description": "Chronic glomerulonephritis + diseases EC", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K02y200", "description": "Chronic focal glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K02y300", "description": "Chronic diffuse glomerulonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K02yz00", "description": "Other chronic glomerulonephritis NOS", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K02z.00", "description": "Chronic glomerulonephritis NOS", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K05..00", "description": "Chronic renal failure", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K050.00", "description": "End stage renal failure", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K05..11", "description": "Chronic uraemia", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K05..12", "description": "End stage renal failure", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K0D..00", "description": "End-stage renal disease", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K100.00", "description": "Chronic pyelonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K100000", "description": "Chronic pyelonephritis without medullary necrosis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K100100", "description": "Chronic pyelonephritis with medullary necrosis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K100200", "description": "Chronic pyelitis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K100300", "description": "Chronic pyonephrosis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K100400", "description": "Nonobstructive reflux-associated chronic pyelonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K100500", "description": "Chronic obstructive pyelonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K100600", "description": "Calculous pyelonephritis", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "K100z00", "description": "Chronic pyelonephritis NOS", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "SP08300", "description": "Kidney transplant failure and rejection", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "TB00100", "description": "Kidney transplant with complication, without blame", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "TB00111", "description": "Renal transplant with complication, without blame", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } }, { "code": "ZV42000", "description": "[V]Kidney transplanted", "attributes": { "Entity type": "res21: CKD", "Category": "diagnostic", "Coding System (Read)": "Read" } } ] } ], "status": 2, "doi": "https://doi.org/10.48533/71z3-d353", "is_deleted": null, "publish_status": 2, "owner": "ieuan.scanlon", "template": { "id": 1, "name": "Clinical-Coded Phenotype", "description": "Phenotype definitions that are based on lists of clinical codes, or algorithms using clinical codes.", "version_id": 1 }, "versions": [ { "version_id": 1020, "version_name": "Chronic Kidney Disease", "version_date": "2021-10-06T16:23:07.788743Z", "is_published": true, "is_latest": true } ] } ]