DGIdb 2.0: mining clinically relevant drug-gene interactions.

Alex H Wagner,Nicholas C Spies,Adam C Coffman,Kilannin Krysiak,Katie M Campbell,Obi L Griffith,Malachi Griffith,Joshua F Mcmichael,Richard K Wilson,Deng Pan,Zachary L Skidmore,Benjamin J Ainscough,James M Eldred,Elaine R Mardis,Jason R Walker

doi:10.1093/nar/gkv1165

Alex H Wagner, Nicholas C Spies + Show 13 more

Open Access

https://doi.org/10.1093/nar/gkv1165

Copy DOI

Abstract

The Drug–Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that consolidates disparate data sources describing drug–gene interactions and gene druggability. It provides an intuitive graphical user interface and a documented application programming interface (API) for querying these data. DGIdb was assembled through an extensive manual curation effort, reflecting the combined information of twenty-seven sources. For DGIdb 2.0, substantial updates have been made to increase content and improve its usefulness as a resource for mining clinically actionable drug targets. Specifically, nine new sources of drug–gene interactions have been added, including seven resources specifically focused on interactions linked to clinical trials. These additions have more than doubled the overall count of drug–gene interactions. The total number of druggable gene claims has also increased by 30%. Importantly, a majority of the unrestricted, publicly-accessible sources used in DGIdb are now automatically updated on a weekly basis, providing the most current information for these sources. Finally, a new web view and API have been developed to allow searching for interactions by drug identifiers to complement existing gene-based search functionality. With these updates, DGIdb represents a comprehensive and user friendly tool for mining the druggable genome for precision medicine hypothesis generation.

Highlights

With the increasing availability and decreasing cost of molecular profiling methods, growing attention has been paid to the use of these technologies for characterizing the mechanisms of human disease at the cohort––and more recently, the individual––level [1,2,3]
DGIdb 2.0 has greatly expanded in content for both drug– gene interactions and druggable gene categories
The numerous sources describing clinical evidence of drug–gene interactions have created a useful resource for reviewing the nature of these interactions in a clinical setting

Summary

Introduction

With the increasing availability and decreasing cost of molecular profiling methods, growing attention has been paid to the use of these technologies for characterizing the mechanisms of human disease at the cohort––and more recently, the individual––level [1,2,3]. DGIdb 1.0 [21] was first introduced as a novel resource to enable mining of multiple existing sources of drug–gene interactions and druggable gene categories. Data describing interactions or potentially druggable categories (referred to as interaction or category claims) from each of these sources were linked to corresponding drug and gene concepts.

Results

Conclusion