Abstract
BackgroundPrecision medicine is a medical approach that takes into account individual genetic variability and often requires Next Generation Sequencing data in order to predict new treatments. Here we present GMIEC, Genomic Modules Identification et Characterization for genomics medicine, an application that is able to identify specific drugs at the level of single patient integrating multi-omics data such as RNA-sequencing, copy-number variation, methylation, Chromatin Immuno-Precipitation and Exome/Whole Genome sequencing. It is also possible to include clinical data related to each patient. GMIEC has been developed as a web-based R-Shiny platform and gives as output a table easy to use and explore.ResultsWe present GMIEC, a Shiny application for genomics medicine. The tool allows the users the integration of two or more multiple omics datasets (e.g. gene-expression, copy-number), at sample level, to identify groups of genes that share common genomic and corresponding drugs. We demonstrate the characteristics of our application by using it to analyze a prostate cancer data set.ConclusionsGMIEC provides a simple interface for genomics medicine. GMIEC was develop with Shiny to provide an application that does not require advanced programming skills. GMIEC consists of three sub-application for the analysis (GMIEC-AN), the visualization (GMIEC-VIS) and the exploration of results (GMIEC-RES). GMIEC is an open source software and is available at https://github.com/guidmt/GMIEC-shiny
Highlights
Precision medicine is a medical approach that takes into account individual genetic variability and often requires Generation Sequencing data in order to predict new treatments
GMIEC provides a Graphical user interface (GUI) interface based on Shiny, but can analyze multiomics datasets in flexible way
When we explored the results of the patients with Active oncogenic modules associated with drugs (AOMDs), these modules were characterized by several up-regulated genes, gains in their copy number status, low levels of methylation, and mutations
Summary
Precision medicine is a medical approach that takes into account individual genetic variability and often requires Generation Sequencing data in order to predict new treatments. Several methods of data fusion exist [1] and many tools were developed to integrate multiple genomic information [2,3,4,5,6,7,8]. These methods are not always straightforward because do not provide graphical. Malagoli Tagliazucchi and Taccioli BMC Genomics (2020) 21:619 section “Installation and Usage” and “Prerequisite” Additional file 1 for details about the installation) It is a web-based R-Shiny tool (www.rstudio.com/shiny) that helps the creation of interactive web pages that can be queried through the use of buttons
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