IGenomicViewer, a Gynecologic Oncology Group software library for the creation of highly customizable, portable, interactive, and linked visualizations of high throughput genomic data

Abstract

e16544 Background: An R software library was created with the goal of creating customizable, platform independent, and portable visualization tools for the annotation, dissemination and interrogation of high dimensioned genomic data. Methods: A set of R functions were created to extend the functionality of the sendplot R library. The functions were applied to BAC aCGH data generated for several GOG studies. Results: The iGenomicViewer function calls created and populated a directory structure which was then ported to a password protected server for interrogation by research team members. The linked html and image output allows users to examine genome wide plots of aberration frequencies and p-values and then drill down to visualizations of regions of interest. Users can interrogate a panel of plots which includes: 1) a heat map of the aCGH data for with tool-tip display of sample and assay specific data (e.g., assay values, sample IDs, and hyperlinks to UCSC browser and sample specific images); 2) a set of interactive annotation tracks which display location of cancer, disease and DNA repair genes; and 3) a plot which displays -log10 p-values and/or aberration frequencies for the BAC assays depicted in the heatmap. For the smallest regions of interest, the panel of plots contains a tiled heatmap which depicts the overlap and gaps in BAC coverage and their alignment with the gene locations represented in the adjacent annotation track. Conclusions: The iGenomicViewer library provides open source software for creation of customizable visualization tools for collaborative research projects involving high dimensioned genomic data. No significant financial relationships to disclose.