EPGA: A Web-Based Information System for Translational Pharmacogenomics.

Kleanthi Lakiotaki,Evgenia Kartsaki,Alexandros Kanterakis,George P Patrinos,George Potamias,Theodora Katsila,Giuseppe Novelli

doi:10.1371/journal.pone.0162801

Kleanthi Lakiotaki, Evgenia Kartsaki + Show 5 more

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https://doi.org/10.1371/journal.pone.0162801

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Abstract

One of the challenges that arise from the advent of personal genomics services is to efficiently couple individual data with state of the art Pharmacogenomics (PGx) knowledge. Existing services are limited to either providing static views of PGx variants or applying a simplistic match between individual genotypes and existing PGx variants. Moreover, there is a considerable amount of haplotype variation associated with drug metabolism that is currently insufficiently addressed. Here, we present a web-based electronic Pharmacogenomics Assistant (ePGA; http://www.epga.gr/) that provides personalized genotype-to-phenotype translation, linked to state of the art clinical guidelines. ePGA's translation service matches individual genotype-profiles with PGx gene haplotypes and infers the corresponding diplotype and phenotype profiles, accompanied with summary statistics. Additional features include i) the ability to customize translation based on subsets of variants of clinical interest, and ii) to update the knowledge base with novel PGx findings. We demonstrate ePGA's functionality on genetic variation data from the 1000 Genomes Project.

Highlights

The roots of the emerging personalized and genome-based medicine can be traced back in the teachings of Hippocrates, the Greek physician and so-called “Father of Western Medicine”
The logical data-model underlying ePGA is based on a star-schema, a very common relational business model for organizing data, which we adopted in the PGx domain
We have developed ePGA, a web based Pharmacogenomics assistant that offers personalized recommendations based on pharmacogenomics evidence and demonstrated how individual genotype profiles are linked to clinical annotations and drug recommendations via genotype to phenotype translation

Summary

Introduction

The roots of the emerging personalized and genome-based medicine can be traced back in the teachings of Hippocrates, the Greek physician and so-called “Father of Western Medicine” From this definite point, to what we call today “the 4Ps of Medicine” (Predictive, Personalized, Preemptive, and Participatory) [1] about 2,500 years have passed and despite the enormous progress in drug development, prescribing the right drug, in the right dose, to the right patient is still not a reality, at least not under a routine clinical framework. Pharmacogenetics, the study of genetic factors that influence drug response and Pharmacogenomics, which study how genome-wide analysis may be used to identify such genetic factors, have greatly advanced over the last decade with more than 19,000 entries for either terms in PubMed (July 2016) We refer to both of them as PGx. PGx has revolutionized drug therapy during the latter half of the 20th century and continues to unearth hundreds of associations between genes and drug response.

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