Abstract
BackgroundBreast cancer comprises multiple tumor entities associated with different biological features and clinical behaviors, making individualized medicine a powerful tool to bring the right drug to the right patient. Next generation sequencing of RNA (RNA-Seq) is a suitable method to detect targets for individualized treatment. Challenges that arise are i) preprocessing and analyzing RNA-Seq data in the n-of-1 setting, ii) extracting clinically relevant and actionable targets from complex data, iii) integrating drug databases, and iv) reporting results to clinicians in a timely and understandable manner.ResultsTo address these challenges, we present OncoRep, an RNA-Seq based n-of-1 reporting tool for breast cancer patients. It reports molecular classification, altered genes and pathways, gene fusions, clinically actionable mutations and drug recommendations. It visualizes the data in an approachable html-based interactive report and a PDF clinical report, providing the clinician and tumor board with a tool to guide the treatment decision making process.ConclusionsOncoRep is free and open-source (https://bitbucket.org/sulab/oncorep/), thereby offering a platform for future development and innovation by the community.
Highlights
Breast cancer comprises multiple tumor entities associated with different biological features and clinical behaviors, making individualized medicine a powerful tool to bring the right drug to the right patient
We developed OncoRep, an open-source RNA-Seq based reporting framework for breast cancer individualized medicine
After the data were processed, the results files from each step and the patient specific meta data were automatically processed by OncoRep to produce a summary report for each patient
Summary
OncoRep was integrated as an RNA-seq Cancer Report pipeline in Omics Pipe [16] which handles the processing of the raw RNA-seq data in an automated and parallel manner on a compute cluster. The report, as displayed here, holds basic patient information, sample processing information and gives a list of FDA approved drugs recommended based on the altered variants, genes and pathways in a patient’s tumor. The QC results and figures are presented within OncoRep. Variant calling Variants identified using the SNPiR pipeline [15] are provided in a tabular format in the HTML report. Visualizations of the pathways are provided with the differentially expressed genes colored based on their log2FoldChange expression compared to normal tissue. The information provided includes 5’ and 3’ fusion partners, fusion description (if available), and the the oncogenic potential prediction depicted as a p-value and expression gain/loss (for details see Implementation). Drug matching OncoRep reports FDA approved compounds that target the discovered differentially expressed genes, variants and pathways in the patient sample. Results are linked to their DrugBank and KEGG Drug entries for further investigation
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