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Epilepsy

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

Type
Disease or Syndrome
ID
PH526
Version ID
1052
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 OXMIS codes
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: 60
Code Description Entity type Coding System (OXMIS Read) Category
667B.00 Nocturnal epilepsy res21: Epilepsy Read diagnostic
F132100 Progressive myoclonic epilepsy res21: Epilepsy Read diagnostic
F25..00 Epilepsy res21: Epilepsy Read diagnostic
F250.00 Generalised nonconvulsive epilepsy res21: Epilepsy Read diagnostic
F250000 Petit mal (minor) epilepsy res21: Epilepsy Read diagnostic
F250011 Epileptic absences res21: Epilepsy Read diagnostic
F250100 Pykno-epilepsy res21: Epilepsy Read diagnostic
F250200 Epileptic seizures - atonic res21: Epilepsy Read diagnostic
F250300 Epileptic seizures - akinetic res21: Epilepsy Read diagnostic
F250500 Lennox-Gastaut syndrome res21: Epilepsy Read diagnostic
F250y00 Other specified generalised nonconvulsive epilepsy res21: Epilepsy Read diagnostic
F250z00 Generalised nonconvulsive epilepsy NOS res21: Epilepsy Read diagnostic
F251.00 Generalised convulsive epilepsy res21: Epilepsy Read diagnostic
F251000 Grand mal (major) epilepsy res21: Epilepsy Read diagnostic
F251011 Tonic-clonic epilepsy res21: Epilepsy Read diagnostic
F251111 Otohara syndrome res21: Epilepsy Read diagnostic
F251200 Epileptic seizures - clonic res21: Epilepsy Read diagnostic
F251300 Epileptic seizures - myoclonic res21: Epilepsy Read diagnostic
F251400 Epileptic seizures - tonic res21: Epilepsy Read diagnostic
F251500 Tonic-clonic epilepsy res21: Epilepsy Read diagnostic
F251y00 Other specified generalised convulsive epilepsy res21: Epilepsy Read diagnostic
F251z00 Generalised convulsive epilepsy NOS res21: Epilepsy Read diagnostic
F252.00 Petit mal status res21: Epilepsy Read diagnostic
F253.00 Grand mal status res21: Epilepsy Read diagnostic
F253.11 Status epilepticus res21: Epilepsy Read diagnostic
F254.00 Partial epilepsy with impairment of consciousness res21: Epilepsy Read diagnostic
F254000 Temporal lobe epilepsy res21: Epilepsy Read diagnostic
F254100 Psychomotor epilepsy res21: Epilepsy Read diagnostic
F254200 Psychosensory epilepsy res21: Epilepsy Read diagnostic
F254300 Limbic system epilepsy res21: Epilepsy Read diagnostic
F254400 Epileptic automatism res21: Epilepsy Read diagnostic
F254500 Complex partial epileptic seizure res21: Epilepsy Read diagnostic
F254z00 Partial epilepsy with impairment of consciousness NOS res21: Epilepsy Read diagnostic
F255.00 Partial epilepsy without impairment of consciousness res21: Epilepsy Read diagnostic
F255000 Jacksonian, focal or motor epilepsy res21: Epilepsy Read diagnostic
F255011 Focal epilepsy res21: Epilepsy Read diagnostic
F255012 Motor epilepsy res21: Epilepsy Read diagnostic
F255100 Sensory induced epilepsy res21: Epilepsy Read diagnostic
F255200 Somatosensory epilepsy res21: Epilepsy Read diagnostic
F255300 Visceral reflex epilepsy res21: Epilepsy Read diagnostic
F255311 Partial epilepsy with autonomic symptoms res21: Epilepsy Read diagnostic
F255400 Visual reflex epilepsy res21: Epilepsy Read diagnostic
F255500 Unilateral epilepsy res21: Epilepsy Read diagnostic
F255600 Simple partial epileptic seizure res21: Epilepsy Read diagnostic
F255y00 Partial epilepsy without impairment of consciousness OS res21: Epilepsy Read diagnostic
F255z00 Partial epilepsy without impairment of consciousness NOS res21: Epilepsy Read diagnostic
F257.00 Kojevnikov's epilepsy res21: Epilepsy Read diagnostic
F25D.00 Menstrual epilepsy res21: Epilepsy Read diagnostic
F25E.00 Stress-induced epilepsy res21: Epilepsy Read diagnostic
F25F.00 Photosensitive epilepsy res21: Epilepsy Read diagnostic
F25X.00 Status epilepticus, unspecified res21: Epilepsy Read diagnostic
F25y.00 Other forms of epilepsy res21: Epilepsy Read diagnostic
F25y000 Cursive (running) epilepsy res21: Epilepsy Read diagnostic
F25y100 Gelastic epilepsy res21: Epilepsy Read diagnostic
F25y200 Locl-rlt(foc)(part)idiop epilep&epilptic syn seiz locl onset res21: Epilepsy Read diagnostic
F25y300 Complex partial status epilepticus res21: Epilepsy Read diagnostic
F25y400 Benign Rolandic epilepsy res21: Epilepsy Read diagnostic
F25yz00 Other forms of epilepsy NOS res21: Epilepsy Read diagnostic
F25z.00 Epilepsy NOS res21: Epilepsy Read diagnostic
SC20000 Traumatic epilepsy res21: Epilepsy Read diagnostic
Rows: 13
Code Description Entity type Coding System (OXMIS Read) Category
2932 PSYCHOSIS EPILEPTIC res21: Epilepsy OXMIS diagnostic
3032EP EPILEPSY ALCOHOLIC res21: Epilepsy OXMIS diagnostic
342 E PARKINSONIAN EPILEPSY res21: Epilepsy OXMIS diagnostic
3450 EPILEPSY NONCONVULSIVE GENERALIZED res21: Epilepsy OXMIS diagnostic
3451 GRAND MAL EPILEPSY res21: Epilepsy OXMIS diagnostic
3453AT EPILEPSY AUTOMATISM res21: Epilepsy OXMIS diagnostic
3453P EPILEPSY PERIPHERAL res21: Epilepsy OXMIS diagnostic
3453T TEMPORAL LOBE EPILEPSY res21: Epilepsy OXMIS diagnostic
3459A POST-TRAUMATIC EPILEPSY res21: Epilepsy OXMIS diagnostic
3459AB ABDOMEN CONVULSIVE EQUIVALENT (EPILEPSY) res21: Epilepsy OXMIS diagnostic
3459BA IDOPATHIC EPILEPSY res21: Epilepsy OXMIS diagnostic
3459D ISCHAEMIC EPILEPSY res21: Epilepsy OXMIS diagnostic
3459N NOCTURNAL EPILEPSY res21: Epilepsy OXMIS diagnostic

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH526/version/1052/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH526/version/1052/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('PH526', '1052', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH526/version/1052/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH526/version/1052/export/codes/?format=json
CSV site_root/phenotypes/PH526/version/1052/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('PH526', '1052', api_client=client)

Version History

Version
ID
Name Owner Publish date
1052 Epilepsy 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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