Genes&Health_PhenotypeCounts
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17 July 2019
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This is a list of current and planned phenotypes from the Genes & Health study (East London Genes & Health, Bradford Genes & Health)
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Here ‘Phenotypes’ means diseases, traits, clinical measurements, prescribing or other clinical information, self-reported information; binary or quantitative; from all types of e-health records, questionnaires or other datasets.
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The data are provided as 'flat' phenotype files, i.e. individual ID followed by a yes/no/unknown or numerical field.
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These 'flat' phenotypes files can then be used directly in statistical analysis e.g. linear regression.
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This is often a simplified version of how the data are represented in the e-health record - for example we might show 'LDL-cholesterol - maximum ever' or 'LDL-cholesterol adjusted for statins'.
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In these cases the actual e-health record data as we have hand-curated it might be a combination of medication over multiple time points, and pathology tests over multiple time points.
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Details of how we have extracted and hand-curated these phenotypes from e-health records, including Read2/CTv3/SNOMED codes included/excluded, ICD10 IC10-CM OPCS4 codes, and other methods used, are available in our Data Dictionary.
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http://www.genesandhealth.org/research/data-dictionary
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For primary care data, we have hand-curated phenotypes - often we have tried to follow the same process as the CALIBER project https://www.ucl.ac.uk/health-informatics/caliber
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For secondary care data, we have automated-phenotypes using ICD10 and ICD10-CM data and PheCodes https://phewascatalog.org/phecodes_icd10
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For secondary care data, we have hand-curated a few phenotypes using ICD10 ICD10-CM data and OPCS data
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Genes & Health takes no responsibility for errors in these data - but if you find these, please point them out to us !
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Thank you ! Bhavi Trivedi, Sarah Finer, David van Heel
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Please see the Data Dictionary for more description of each phenotype:
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http://www.genesandhealth.org/research/data-dictionary
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Please see the Cohort Profile for more details:
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https://www.biorxiv.org/content/10.1101/426163v2
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We are currently (17 July 2019) updating the following:
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primary care clinical and laboratory measurements
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Future Plans
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MINAP / NICOR national cardiovascular datasets
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ELFT Mental Health datasets
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NHS Digital: National Hospital Episode Statistics & Mortality
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add Bradford primary and secondary care health data
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merged phenotypes (e.g. diabetes can be coded in stage 1 questionnaire, primary care, secondary care, and national HES datasets !)
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