title: Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin.
abstract: OBJECTIVE
  DNA 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.
  
  
  METHODS
  A 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.
  
  
  RESULTS
  The 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.
authors.affiliation: Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA. hua.xu@vanderbilt.edu
authors.forename: Hua
authors.initials: H
authors.lastname: Xu
authors.forename: Min
authors.initials: M
authors.lastname: Jiang
authors.forename: Matt
authors.initials: M
authors.lastname: Oetjens
authors.forename: Erica A
authors.initials: EA
authors.lastname: Bowton
authors.forename: Andrea H
authors.initials: AH
authors.lastname: Ramirez
authors.forename: Janina M
authors.initials: JM
authors.lastname: Jeff
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Basford
authors.forename: Jill M
authors.initials: JM
authors.lastname: Pulley
authors.forename: James D
authors.initials: JD
authors.lastname: Cowan
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Wang
authors.forename: Marylyn D
authors.initials: MD
authors.lastname: Ritchie
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Masys
authors.forename: Dan M
authors.initials: DM
authors.lastname: Roden
authors.forename: Dana C
authors.initials: DC
authors.lastname: Crawford
authors.forename: Joshua C
authors.initials: JC
authors.lastname: Denny
mesh_terms: D000465:Algorithms; D000925:Anticoagulants / Q000008:administration & dosage*; D001189:Aryl Hydrocarbon Hydroxylases / Q000235:genetics; D065729:Cytochrome P-450 CYP2C9; D057225:Data Mining / Q000379:methods*; D030561:Databases, Nucleic Acid; D054796:Drug Dosage Calculations; D057286:Electronic Health Records; D055106:Genome-Wide Association Study; D006801:Humans; D016014:Linear Models; D006899:Mixed Function Oxygenases / Q000235:genetics; D009323:Natural Language Processing; D010597:Pharmacogenetics; D057285:Precision Medicine; D014481:United States; D064417:Vitamin K Epoxide Reductases; D014859:Warfarin / Q000008:administration & dosage*
chemical_list: D000925:Anticoagulants; D014859:Warfarin; D006899:Mixed Function Oxygenases; C450260:CYP2C9 protein, human; D065729:Cytochrome P-450 CYP2C9; D001189:Aryl Hydrocarbon Hydroxylases; C578523:VKORC1 protein, human; D064417:Vitamin K Epoxide Reductases