[ { "phenotype_id": "PH564", "phenotype_version_id": 1128, "name": "Stroke", "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": "2021-10-06T16:25:00.866255Z", "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": "2021-10-06T16:25:00.866283Z", "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 }, { "name": "OXMIS codes", "value": 15 } ], "event_date_range": "01/04/2000 - 31/03/2012", "concept_information": [ { "concept_id": 1960, "concept_version_id": 5058, "concept_name": "Stroke - Primary Care", "coding_system": { "id": 5, "name": "Read codes v2", "description": "Read codes v2" }, "phenotype_id": "PH564", "phenotype_version_id": 1128, "phenotype_name": "Stroke", "code_attribute_header": [ "Entity type", "Coding System (OXMIS Read)", "Category" ], "codes": [ { "code": "G61..00", "description": "Intracerebral haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G610.00", "description": "Cortical haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G611.00", "description": "Internal capsule haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G61..11", "description": "CVA - cerebrovascular accid due to intracerebral haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G61..12", "description": "Stroke due to intracerebral haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G612.00", "description": "Basal nucleus haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G613.00", "description": "Cerebellar haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G614.00", "description": "Pontine haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G615.00", "description": "Bulbar haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G616.00", "description": "External capsule haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G618.00", "description": "Intracerebral haemorrhage, multiple localized", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G61X.00", "description": "Intracerebral haemorrhage in hemisphere, unspecified", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G61X000", "description": "Left sided intracerebral haemorrhage, unspecified", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G61X100", "description": "Right sided intracerebral haemorrhage, unspecified", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G61z.00", "description": "Intracerebral haemorrhage NOS", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G63y000", "description": "Cerebral infarct due to thrombosis of precerebral arteries", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G63y100", "description": "Cerebral infarction due to embolism of precerebral arteries", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64..00", "description": "Cerebral arterial occlusion", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G640.00", "description": "Cerebral thrombosis", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G640000", "description": "Cerebral infarction due to thrombosis of cerebral arteries", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G641.00", "description": "Cerebral embolism", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G641000", "description": "Cerebral infarction due to embolism of cerebral arteries", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64..11", "description": "CVA - cerebral artery occlusion", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G641.11", "description": "Cerebral embolus", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64..12", "description": "Infarction - cerebral", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64..13", "description": "Stroke due to cerebral arterial occlusion", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64z.00", "description": "Cerebral infarction NOS", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64z000", "description": "Brainstem infarction", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64z100", "description": "Wallenberg syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64z.11", "description": "Brainstem infarction NOS", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64z111", "description": "Lateral medullary syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64z.12", "description": "Cerebellar infarction", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64z200", "description": "Left sided cerebral infarction", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64z300", "description": "Right sided cerebral infarction", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G64z400", "description": "Infarction of basal ganglia", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G65..00", "description": "Transient cerebral ischaemia", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G650.00", "description": "Basilar artery syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G650.11", "description": "Insufficiency - basilar artery", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G651.00", "description": "Vertebral artery syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G651000", "description": "Vertebro-basilar artery syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G65..11", "description": "Drop attack", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G65..12", "description": "Transient ischaemic attack", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G65..13", "description": "Vertebro-basilar insufficiency", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G652.00", "description": "Subclavian steal syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G653.00", "description": "Carotid artery syndrome hemispheric", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G654.00", "description": "Multiple and bilateral precerebral artery syndromes", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G656.00", "description": "Vertebrobasilar insufficiency", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G65y.00", "description": "Other transient cerebral ischaemia", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G65z.00", "description": "Transient cerebral ischaemia NOS", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G65z000", "description": "Impending cerebral ischaemia", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G65z100", "description": "Intermittent cerebral ischaemia", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G65zz00", "description": "Transient cerebral ischaemia NOS", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G66..00", "description": "Stroke and cerebrovascular accident unspecified", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G660.00", "description": "Middle cerebral artery syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G661.00", "description": "Anterior cerebral artery syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G66..11", "description": "CVA unspecified", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G66..12", "description": "Stroke unspecified", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G66..13", "description": "CVA - Cerebrovascular accident unspecified", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G662.00", "description": "Posterior cerebral artery syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G663.00", "description": "Brain stem stroke syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G664.00", "description": "Cerebellar stroke syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G665.00", "description": "Pure motor lacunar syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G666.00", "description": "Pure sensory lacunar syndrome", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G667.00", "description": "Left sided CVA", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G668.00", "description": "Right sided CVA", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G6W..00", "description": "Cereb infarct due unsp occlus/stenos precerebr arteries", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "G6X..00", "description": "Cerebrl infarctn due/unspcf occlusn or sten/cerebrl artrs", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "Gyu6200", "description": "[X]Other intracerebral haemorrhage", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "Gyu6300", "description": "[X]Cerebrl infarctn due/unspcf occlusn or sten/cerebrl artrs", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "Gyu6400", "description": "[X]Other cerebral infarction", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "Gyu6500", "description": "[X]Occlusion and stenosis of other precerebral arteries", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "Gyu6600", "description": "[X]Occlusion and stenosis of other cerebral arteries", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "Gyu6G00", "description": "[X]Cereb infarct due unsp occlus/stenos precerebr arteries", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "L440.11", "description": "CVA - cerebrovascular accident in the puerperium", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } }, { "code": "L440.12", "description": "Stroke in the puerperium", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "Read", "Category": "diagnostic" } } ] }, { "concept_id": 1961, "concept_version_id": 5060, "concept_name": "Stroke - Primary Care", "coding_system": { "id": 15, "name": "OXMIS codes", "description": "OXMIS codes" }, "phenotype_id": "PH564", "phenotype_version_id": 1128, "phenotype_name": "Stroke", "code_attribute_header": [ "Entity type", "Coding System (OXMIS Read)", "Category" ], "codes": [ { "code": "4350AT", "description": "TRANSIENT ISCHAEMIC ATTACKS WITH HYPERTE", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "OXMIS", "Category": "diagnostic" } }, { "code": "4359AT", "description": "TRANSIENT ISCHAEMIC ATTACKS", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "OXMIS", "Category": "diagnostic" } }, { "code": "4360A", "description": "CEREBROVASCULAR ACCIDENT WITH HYPERTENSI", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "OXMIS", "Category": "diagnostic" } }, { "code": "4360B", "description": "STROKE WITH HYPERTENSION", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "OXMIS", "Category": "diagnostic" } }, { "code": "4369A", "description": "CVA (CEREBROVASCULAR ACCIDENT)", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "OXMIS", "Category": "diagnostic" } }, { "code": "4369AL", "description": "CEREBROVASCULAR ACCIDENT LEFT", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "OXMIS", "Category": "diagnostic" } }, { "code": "4369AR", "description": "CEREBROVASCULAR ACCIDENT RIGHT", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "OXMIS", "Category": "diagnostic" } }, { "code": "4369B", "description": "STROKE", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "OXMIS", "Category": "diagnostic" } }, { "code": "4369BN", "description": "SYNDROME STROKE", "attributes": { "Entity type": "res21: Stroke", "Coding System (OXMIS Read)": "OXMIS", "Category": "diagnostic" } } ] } ], "status": 2, "doi": "https://doi.org/10.48533/pdx6-3981", "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": 1128, "version_name": "Stroke", "version_date": "2021-10-06T16:25:00.897698Z", "is_published": true, "is_latest": true } ] } ]