ArticleJournal of the American Medical Informatics Association : JAMIA
Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin.
Article in Journal of the American Medical Informatics Association : JAMIA. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 2 of them syntheses that pooled it.
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Who cites it
52 citing papers in PubMed, 2 syntheses or guidelines pooled it, 85 citations in OpenAlex.
- Methods for the Analysis and Interpretation for Rare Variants Associated with Complex Traits.Current protocols in human genetics · 2019Pooled it
- SLCO1B1 genetic variant associated with statin-induced myopathy: a proof-of-concept study using the clinical practice research datalink.Clinical pharmacology and therapeutics · 2013Pooled it
- Personalised health plan development using agentic AI in Singapore's national preventive care programme: a pilot study.NPJ digital medicine · 2026Article
- Artificial intelligence and machine learning for precision warfarin dosing: a comprehensive narrative review.European journal of clinical pharmacology · 2026Review
- Using electronic health records for clinical pharmacology research: Challenges and considerations.Clinical and translational science · 2024Review
- Artificial intelligence in sepsis early prediction and diagnosis using unstructured data in healthcare.Nature communications · 2021Article
- Clinical concept extraction: A methodology review.Journal of biomedical informatics · 2020Review
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- Assessment of the impact of EHR heterogeneity for clinical research through a case study of silent brain infarction.BMC medical informatics and decision making · 2020Article
- Renin-Angiotensin-Aldosterone System Modulates Blood Pressure Response During Vascular Endothelial Growth Factor Receptor Inhibition.JACC. CardioOncology · 2019Article
- Natural Language Processing for the Identification of Silent Brain Infarcts From Neuroimaging Reports.JMIR medical informatics · 2019Article
- Replicating medication trend studies using ad hoc information extraction in a clinical data warehouse.BMC medical informatics and decision making · 2019Article
- A clinical text classification paradigm using weak supervision and deep representation.BMC medical informatics and decision making · 2019Article
- PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies.Journal of the American Medical Informatics Association : JAMIA · 2018Article
- The use of electronic health records for psychiatric phenotyping and genomics.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2018Review
- Characterization of Statin Low-Density Lipoprotein Cholesterol Dose-Response Using Electronic Health Records in a Large Population-Based Cohort.Circulation. Genomic and precision medicine · 2018Article
- Article
- Clinical information extraction applications: A literature review.Journal of biomedical informatics · 2018Review
- Clinical Informatics Researcher's Desiderata for the Data Content of the Next Generation Electronic Health Record.Applied clinical informatics · 2017Article
- HealthRecSys: A semantic content-based recommender system to complement health videos.BMC medical informatics and decision making · 2017Article
Corrections and comments
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Authors and funding
15 authors at 2 institutions in 1 country.
Funding
Abstract
objectiveDNA biobanks linked to comprehensive electronic health records systems are potentially powerful resources for pharmacogenetic studies. This study sought to develop natural-language-processing algorithms to extract drug-dose information from clinical text, and to assess the capabilities of such tools to automate the data-extraction process for pharmacogenetic studies. MATERIALS AND
methodsA manually validated warfarin pharmacogenetic study identified a cohort of 1125 patients with a stable warfarin dose, in which 776 patients were managed by Coumadin Clinic physicians, and the remaining 349 patients were managed by their providers. The authors developed two algorithms to extract weekly warfarin doses from both data sets: a regular expression-based program for semistructured Coumadin Clinic notes; and an advanced weekly dose calculator based on an existing medication information extraction system (MedEx) for narrative providers' notes. The authors then conducted an association analysis between an automatically extracted stable weekly dose of warfarin and four genetic variants of VKORC1 and CYP2C9 genes. The performance of the weekly dose-extraction program was evaluated by comparing it with a gold standard containing manually curated weekly doses. Precision, recall, F-measure, and overall accuracy were reported. Associations between known variants in VKORC1 and CYP2C9 and warfarin stable weekly dose were performed with linear regression adjusted for age, gender, and body mass index.
resultsThe authors' evaluation showed that the MedEx-based system could determine patients' warfarin weekly doses with 99.7% recall, 90.8% precision, and 93.8% accuracy. Using the automatically extracted weekly doses of warfarin, the authors successfully replicated the previous known associations between warfarin stable dose and genetic variants in VKORC1 and CYP2C9.
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