SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads
| Autor: | Zengquan He, Wenqian Zhang, Songbo Huang, Jikun Wu, Jun Wang, Tak-Wah Lam, Yanbing Cheng, Siu-Ming Yiu, Zhiyu Peng |
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| Rok vydání: | 2013 |
| Předmět: |
Statistics and Probability
Sequence analysis Molecular Sequence Data RNA-Seq Computational biology Biology computer.software_genre Biochemistry Fusion gene symbols.namesake Neoplasms Sequence Homology Nucleic Acid Humans Base sequence Molecular Biology Gene Sanger sequencing Fusion Base Sequence Sequence Analysis RNA RNA Computational Biology High-Throughput Nucleotide Sequencing Computer Science Applications Computational Mathematics Computational Theory and Mathematics symbols Data mining Gene Fusion computer Algorithms Software |
| Zdroj: | Bioinformatics (Oxford, England). 29(23) |
| ISSN: | 1367-4811 |
| Popis: | 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. Availability: http://soap.genomics.org.cn/SOAPfusion.html Contact: smyiu@cs.hku.hk Supplementary information: Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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