Jikun Wu1, Wenqian Zhang, Songbo Huang, Zengquan He, Yanbing Cheng, Jun Wang, Tak-Wah Lam, Zhiyu Peng, Siu-Ming Yiu. 1. Department of Computer Science, The University of Hong Kong, Hong Kong, China, BGI-Shenzhen, Shenzhen, China, Department of Biology, University of Copenhagen, Copenhagen, Denmark, King Abdulaziz University, Jeddah, Saudi Arabia, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen and Guangzhou Key Laboratory of Cancer Trans-Omics Research, BGI-Guangzhou, Guangzhou, China.
Abstract
MOTIVATION: RNA-Seq provides a powerful approach to carry out ab initio investigation of fusion transcripts representing critical translocation and post-transcriptional events that recode hereditary information. Most of the existing computational fusion detection tools are challenged by the issues of accuracy and how to handle multiple mappings. RESULTS: We present a novel tool SOAPfusion for fusion discovery with paired-end RNA-Seq reads. SOAPfusion is accurate and efficient for fusion discovery with high sensitivity (≥93%), low false-positive rate (≤1.36%), even the coverage is as low as 10×, highlighting its ability to detect fusions efficiently at low sequencing cost. From real data of Universal Human Reference RNA (UHRR) samples, SOAPfusion detected 7 novel fusion genes, more than other existing tools and all genes have been validated through reverse transcription-polymerase chain reaction followed by Sanger sequencing. SOAPfusion thus proves to be an effective method with precise applicability in search of fusion transcripts, which is advantageous to accelerate pathological and therapeutic cancer studies.
MOTIVATION: RNA-Seq provides a powerful approach to carry out ab initio investigation of fusion transcripts representing critical translocation and post-transcriptional events that recode hereditary information. Most of the existing computational fusion detection tools are challenged by the issues of accuracy and how to handle multiple mappings. RESULTS: We present a novel tool SOAPfusion for fusion discovery with paired-end RNA-Seq reads. SOAPfusion is accurate and efficient for fusion discovery with high sensitivity (≥93%), low false-positive rate (≤1.36%), even the coverage is as low as 10×, highlighting its ability to detect fusions efficiently at low sequencing cost. From real data of Universal Human Reference RNA (UHRR) samples, SOAPfusion detected 7 novel fusion genes, more than other existing tools and all genes have been validated through reverse transcription-polymerase chain reaction followed by Sanger sequencing. SOAPfusion thus proves to be an effective method with precise applicability in search of fusion transcripts, which is advantageous to accelerate pathological and therapeutic cancer studies.
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