ArticlePloS one2022
Reproducible disease phenotyping at scale: Example of coronary artery disease in UK Biobank.
Article in PloS one, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 13 citations in OpenAlex.
- No evidence for genotype-treatment interactions with breast cancer endocrine therapy adverse effects in UK Biobank.NPJ breast cancer · 2026Article
- Evaluating genotype-treatment interactions for high-risk medications in British general practice: a retrospective cohort study using UK Biobank.The British journal of general practice : the journal of the Royal College of General Practitioners · 2026Article
- Blood pressure, plasma proteins, and cardiovascular diseases: a network Mendelian randomization and observational study.European heart journal · 2026Observational
- Association Between Therapeutic Inertia and Future Hypoglycemia Among Patients with Type 2 Diabetes.Diabetes epidemiology and management · 2026Article
- Artificial intelligence in precision medicine: transforming disease subtyping, medical imaging, and pharmacogenomics.Emerging topics in life sciences · 2025Article
- Multi-domain rule-based phenotyping algorithms enable improved GWAS signal.NPJ digital medicine · 2025Article
- A computational framework for defining and validating reproducible phenotyping algorithms of 313 diseases in the UK Biobank.Scientific reports · 2025Article
- Characteristics of insulin prescriptions and their association with glycemic control in adults with type 2 diabetes mellitus.Diabetes epidemiology and managementArticle
- Examining therapeutic inertia patterns in type 2 diabetes patients with multiple chronic conditions: Time-to-event analysis.Journal of multimorbidity and comorbidityArticle
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Authors and funding
10 authors at 5 institutions in 1 country.
Funding
Abstract
importanceA lack of internationally agreed standards for combining available data sources at scale risks inconsistent disease phenotyping limiting research reproducibility.
objectiveTo develop and then evaluate if a rules-based algorithm can identify coronary artery disease (CAD) sub-phenotypes using electronic health records (EHR) and questionnaire data from UK Biobank (UKB).
designCase-control and cohort study.
settingProspective cohort study of 502K individuals aged 40-69 years recruited between 2006-2010 into the UK Biobank with linked hospitalization and mortality data and genotyping.
participantsWe included all individuals for phenotyping into 6 predefined CAD phenotypes using hospital admission and procedure codes, mortality records and baseline survey data. Of these, 408,470 unrelated individuals of European descent had a polygenic risk score (PRS) for CAD estimated. EXPOSURE: CAD Phenotypes. MAIN OUTCOMES AND MEASURES: Association with baseline risk factors, mortality (n = 14,419 over 7.8 years median f/u), and a PRS for CAD.
resultsThe algorithm classified individuals with CAD into prevalent MI (n = 4,900); incident MI (n = 4,621), prevalent CAD without MI (n = 10,910), incident CAD without MI (n = 8,668), prevalent self-reported MI (n = 2,754); prevalent self-reported CAD without MI (n = 5,623), yielding 37,476 individuals with any type of CAD. Risk factors were similar across the six CAD phenotypes, except for fewer men in the self-reported CAD without MI group (46.7% v 70.1% for the overall group). In age- and sex- adjusted survival analyses, mortality was highest following incident MI (HR 6.66, 95% CI 6.07-7.31) and lowest for prevalent self-reported CAD without MI at baseline (HR 1.31, 95% CI 1.15-1.50) compared to disease-free controls. There were similar graded associations across the six phenotypes per SD increase in PRS, with the strongest association for prevalent MI (OR 1.50, 95% CI 1.46-1.55) and the weakest for prevalent self-reported CAD without MI (OR 1.08, 95% CI 1.05-1.12). The algorithm is available in the open phenotype HDR UK phenotype library (https://portal.caliberresearch.org/).
conclusionsAn algorithmic, EHR-based approach distinguished six phenotypes of CAD with distinct survival and PRS associations, supporting adoption of open approaches to help standardize CAD phenotyping and its wider potential value for reproducible research in other conditions.
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