CREDO: Highly confident disease-relevant A-to-I RNA-editing discovery in breast cancer

Woochang Hwang, Stefano Calza, Marco Silvestri, Yudi Pawitan, Youngjo Lee

Research output: Contribution to journalArticlepeer-review

Abstract

Adenosine-to-Inosine (A-to-I) RNA editing is the most prevalent post-transcriptional modification of RNA molecules. Researchers have attempted to find reliable RNA editing using next generation sequencing (NGS) data. However, most of these attempts suffered from a high rate of false positives, and they did not consider the clinical relevance of the identified RNA editing, for example, in disease progression. We devised an effective RNA-editing discovery pipeline called CREDO, which includes novel statistical filtering modules based on integration of DNA- and RNA-seq data from matched tumor-normal tissues. CREDO was compared with three other RNA-editing discovery pipelines and found to give significantly fewer false positives. Application of CREDO to breast cancer data from the Cancer Genome Atlas (TCGA) project discovered highly confident RNA editing with clinical relevance to cancer progression in terms of patient survival. RNA-editing detection using DNA- and RNA-seq data from matched tumor-normal tissues should be more routinely performed as multiple omics data are becoming commonly available from each patient sample. We believe CREDO is an effective and reliable tool for this problem.

Original languageEnglish
Article number5064
JournalScientific Reports
Volume9
Issue number1
DOIs
Publication statusPublished - Dec 1 2019

ASJC Scopus subject areas

  • General

Fingerprint

Dive into the research topics of 'CREDO: Highly confident disease-relevant A-to-I RNA-editing discovery in breast cancer'. Together they form a unique fingerprint.

Cite this