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. 2021 Jan;109(1):116-122.
doi: 10.1002/cpt.2067. Epub 2020 Oct 24.

PharmGKB Tutorial for Pharmacogenomics of Drugs Potentially Used in the Context of COVID-19

Rachel Huddart  1 , Michelle Whirl-Carrillo  1 , Russ B Altman  1   2   3   4 , Teri E Klein  1   4
Affiliations

PharmGKB Tutorial for Pharmacogenomics of Drugs Potentially Used in the Context of COVID-19

Rachel Huddart et al. Clin Pharmacol Ther. 2021 Jan.

Abstract

Pharmacogenomics (PGx) is a key area of precision medicine, which is already being implemented in some health systems and may help guide clinicians toward effective therapies for individual patients. Over the last 2 decades, the Pharmacogenomics Knowledgebase (PharmGKB) has built a unique repository of PGx knowledge, including annotations of clinical guideline and regulator-approved drug labels in addition to evidence-based drug pathways and annotations of the scientific literature. All of this knowledge is freely accessible on the PharmGKB website. In the first of a series of PharmGKB tutorials, we introduce the PharmGKB coronavirus disease 2019 (COVID-19) portal and, using examples of drugs found in the portal, demonstrate some of the main features of PharmGKB. This paper is intended as a resource to help users become quickly acquainted with the wealth of information stored in PharmGKB.

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Conflict of interest statement

R.B.A. is a stockholder in Personalis, 23andMe, and Youscript. All other authors declared no competing interests for this work.

Figures

Figure 1
Figure 1
Image of the Pharmacogenomics Knowledgebase (PharmGKB) drug page for fluvoxamine. The tabs on the left side of the page list the different resources provided by PharmGKB. The existence of resources specific to fluvoxamine is indicated by a blue dot next to the resource name.
Figure 2
Figure 2
Image of all of the drug label annotations in Pharmacogenomics Knowledgebase (PharmGKB) for fluvoxamine. PGx, pharmacogenomics.
Figure 3
Figure 3
Pharmacogenomics Knowledgebase (PharmGKB) clinical annotation for fentanyl and the CYP3A4*1 and *1G alleles.
Figure 4
Figure 4
Image of the genotype picker tool on the annotation page for the Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for sertraline. Selecting the *2/*2 genotype retrieves the specific recommendations for a CYP2C19 poor metabolizer. PharmGKB, Pharmacogenomics Knowledgebase.
Figure 5
Figure 5
The Pharmacogenomics Knowledgebase (PharmGKB) haloperidol pathway, pharmacokinetics. The original, interactive pathway can be accessed at https://www.pharmgkb.org/pathway/PA166163828.
Figure 6
Figure 6
The Pharmacogenomics Knowledgebase (PharmGKB) anti‐arrhythmic pathway, pharmacodynamics. The original, interactive pathway can be accessed at https://www.pharmgkb.org/pathway/PA2033.
See this image and copyright information in PMC

References

    1. Whirl‐Carrillo, M. et al. Pharmacogenomics knowledge for personalized medicine. Clin. Pharma. Ther. 92, 414–417 (2012). - PMC - PubMed
    1. Lever, J. et al. PGxMine: text mining for curation of PharmGKB. Pacific Symp. Biocom. 25, 611–622 (2020). - PMC - PubMed
    1. Back, D. et al. COVID‐19 treatment in patients with comorbidities: awareness of drug‐drug interactions. Br. J. Clin. Pharmacol 10.1111/bcp.14358. [e‐pub ahead of print]. - DOI - PMC - PubMed
    1. PharmGKB . Drug label information and legend <https://www.pharmgkb.org/page/drugLabelLegend> (2020). Accessed August 10, 2020.
    1. PharmGKB . Clinical annotation levels of evidence <https://www.pharmgkb.org/page/clinAnnLevels> (2020). Accessed August 10, 2020.

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