title: Evaluation of the PharmGKB knowledge base as a resource for efficiently assessing the clinical validity and utility of pharmacogenetic assays.
abstract: Prior to clinical use, pharmacogenetic tests should be systematically evaluated for their clinical validity and utility. Here, we evaluated whether the publicly available, online Pharmacogenomics Knowledge Base (PharmGKB) could facilitate such assessments by efficiently identifying relevant peer-reviewed manuscripts. The search targets were 55 manuscripts regarding clinical validity and utility included in systematic reviews of warfarin, antidepressant, and irinotecan pharmacogenetics. When direct inclusion in PharmGKB was the search criterion, recall was 33% and precision was 16%. However, recall increased to 78% when citation within a PharmGKB-identified manuscript was added as a search criterion. These recalled manuscripts accounted for 87% of the study subjects, and domain experts determined that the omission of the remaining manuscripts was unlikely to have changed the conclusions of the reviews. Thus, we conclude that PharmGKB can facilitate the systematic assessment of pharmacogenetic assays through the efficient identification of relevant peer-reviewed manuscripts.
authors.affiliation: Division of Clinical Informatics, Department of Community and Family Medicine, Duke University, Durham, NC, USA.
authors.forename: Kensaku
authors.initials: K
authors.lastname: Kawamoto
authors.forename: Lori A
authors.initials: LA
authors.lastname: Orlando
authors.forename: Deepak
authors.initials: D
authors.lastname: Voora
authors.forename: David F
authors.initials: DF
authors.lastname: Lobach
authors.forename: Scott
authors.initials: S
authors.lastname: Joy
authors.forename: Alex
authors.initials: A
authors.lastname: Cho
authors.forename: Geoffrey S
authors.initials: GS
authors.lastname: Ginsburg
mesh_terms: D005820:Genetic Testing; D006801:Humans; D051188:Knowledge Bases; D010597:Pharmacogenetics; D015203:Reproducibility of Results