title: Genomic variant annotation workflow for clinical applications.
abstract: Annotation and interpretation of DNA aberrations identified through next-generation sequencing is becoming an increasingly important task. Even more so in the context of data analysis pipelines for medical applications, where genomic aberrations are associated with phenotypic and clinical features. Here we describe a workflow to identify potential gene targets in aberrated genes or pathways and their corresponding drugs. To this end, we provide the R/Bioconductor package rDGIdb, an R wrapper to query the drug-gene interaction database (DGIdb). DGIdb accumulates drug-gene interaction data from 15 different resources and allows filtering on different levels. The rDGIdb package makes these resources and tools available to R users. Moreover, rDGIdb queries can be automated through incorporation of the rDGIdb package into NGS sequencing pipelines.
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Thurnherr
authors.affiliation: SIB Swiss Institute of Bioinformatics, Basel, Switzerland; NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland.
authors.forename: Franziska
authors.initials: F
authors.lastname: Singer
authors.affiliation: SIB Swiss Institute of Bioinformatics, Basel, Switzerland; NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Stekhoven
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Niko
authors.initials: N
authors.lastname: Beerenwinkel
keywords: Bioconductor package; Drug-gene interaction; annotation; clinical application; genomics; next-generation sequencing; pipeline.; somatic variant