PG-path: Modeling and personalizing pharmacogenomics-based pathways

PLoS One. 2020 May 4;15(5):e0230950. doi: 10.1371/journal.pone.0230950. eCollection 2020.

Abstract

A pharmacogenomics-based pathway represents a series of reactions that occur between drugs and genes in the human body after drug administration. PG-path is a pharmacogenomics-based pathway that standardizes and visualizes the components (nodes) and actions (edges) involved in pharmacokinetic and pharmacodynamic processes. It provides an intuitive understanding of the drug response in the human body. A pharmacokinetic pathway visualizes the absorption, distribution, metabolism, and excretion (ADME) at the systemic level, and a pharmacodynamic pathway shows the action of the drug in the target cell at the cellular-molecular level. The genes in the pathway are displayed in locations similar to those inside the body. PG-path allows personalized pathways to be created by annotating each gene with the overall impact degree of deleterious variants in the gene. These personalized pathways play a role in assisting tailored individual prescriptions by predicting changes in the drug concentration in the plasma. PG-path also supports counseling for personalized drug therapy by providing visualization and documentation.

MeSH terms

  • Computational Biology / methods*
  • Databases, Genetic
  • Drug Therapy / methods
  • Drug-Related Side Effects and Adverse Reactions / genetics
  • Drug-Related Side Effects and Adverse Reactions / metabolism
  • Gastrointestinal Absorption / genetics
  • Genetic Association Studies
  • Humans
  • Inactivation, Metabolic / drug effects
  • Inactivation, Metabolic / genetics
  • Information Storage and Retrieval / methods
  • Metabolic Networks and Pathways / drug effects
  • Metabolic Networks and Pathways / genetics*
  • Models, Theoretical
  • Pharmaceutical Preparations / metabolism*
  • Pharmacogenetics / methods*
  • Precision Medicine / methods*
  • Software*

Substances

  • Pharmaceutical Preparations

Grants and funding

There is no funding associated with this study. This study was conducted as a Ph.D. thesis work of the first author at Seoul National University College of Medicine. No funder has a role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.