Epione application: An integrated web‑toolkit of clinical genomics and personalized medicine in systemic lupus erythematosus

Abstract

Genome wide association studies (GWAS) have identified autoimmune disease‑associated loci, a number of which are involved in numerous disease‑associated pathways. However, much of the underlying genetic and pathophysi‑ ological mechanisms remain to be elucidated. Systemic lupus erythematosus (SLE) is a chronic, highly heterogeneous auto‑ immune disease, characterized by differences in autoantibody profile, serum cytokines and a multi‑system involvement. This study presents the Epione application, an integrated bioinformatics web‑toolkit, designed to assist medical experts and researchers in more accurately diagnosing SLE. The application aims to identify the most credible gene variants and single nucleotide polymorphisms (SNPs) associated with SLE susceptibility, by using patient's genomic data to aid the medical expert in SLE diagnosis. The application contains useful knowledge of >70,000 SLE‑related publications that have been analyzed, using data mining and semantic tech‑ niques, towards extracting the SLE‑related genes and the corresponding SNPs. Probable genes associated with the patient's genomic profile are visualized with several graphs, including chromosome ideograms, statistic bars and regulatory networks through data mining studies with relative publica‑ tions, to obtain a representative number of the most credible candidate genes and biological pathways associated with the SLE. Furthermore, an evaluation study was performed on a patient diagnosed with SLE and is presented herein. Epione has also been expanded in family‑related candidate patients to evaluate its predictive power. All the recognized gene variants that were previously considered to be associated with SLE were accurately identified in the output profile of the patient, and by comparing the results, novel findings have emerged. The Epione application may assist and facilitate in early stage diagnosis by using the patients' genomic profile to compare against the list of the most predictable candidate gene variants related to SLE. Its diagnosis‑oriented output presents the user with a structured set of results on variant association, posi‑ tion in genome and links to specific bibliography and gene network associations. The overall aim of the present study was to provide a reliable tool for the most effective study of SLE. This novel and accessible webserver tool of SLE is available at http://geneticslab.aua.gr/epione/.