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Clin Pharmacol Ther. 2019 Jul 15. doi: 10.1002/cpt.1568. [Epub ahead of print]

Pharmacogenomics Clinical Annotation Tool (PharmCAT).

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Department of Biomedical Data Science, Stanford University, Palo Alto, CA, 94305, USA.
Biomedical Informatics Training Program, Stanford University, Palo Alto, CA, 94305.
Departments of Biomedical Data Science, Biomedical Engineering, Genetics and Medicine, Stanford University, Palo Alto, CA, 94305, USA.
formerly Department of Genetics, Stanford University, Palo Alto, CA, 94305.
Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Department of Biomedical Data Science and Biomedical Informatics Research, School of Medicine, Stanford University, Palo Alto, CA, 94305.


Pharmacogenomics (PGx) decision support and return of results is an active area of precision medicine. One challenge of implementing PGx is extracting genomic variants and assigning haplotypes in order to apply prescribing recommendations and information from CPIC, FDA, PharmGKB, etc. PharmCAT (1) extracts variants specified in guidelines from a genetic dataset derived from sequencing or genotyping technologies; (2) infers haplotypes and diplotypes; and (3) generates a report containing genotype/diplotype-based annotations and guideline recommendations. We describe PharmCAT and a pilot validation project comparing results for 1000 Genomes sequences of Coriell samples with corresponding Genetic Testing Reference Materials Coordination Program (GeT-RM) sample characterization. PharmCAT was highly concordant with the GeT-RM data. PharmCAT is available in GitHub to evaluate, test and report results back to the community. As precision medicine becomes more prevalent, our ability to consistently, accurately, and clearly define and report PGx annotations and prescribing recommendations is critical. This article is protected by copyright. All rights reserved.


CPIC ; Pharmacogenetics; bioinformatics pipeline; pharmacogenomics


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