SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.
Bioinformatics
; 29(23): 2971-8, 2013 Dec 01.
Article
de En
| MEDLINE
| ID: mdl-24123671
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.
Texte intégral:
1
Collection:
01-internacional
Base de données:
MEDLINE
Sujet principal:
Logiciel
/
Fusion de gènes
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Séquençage nucléotidique à haut débit
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Tumeurs
Limites:
Humans
Langue:
En
Journal:
Bioinformatics
Sujet du journal:
INFORMATICA MEDICA
Année:
2013
Type de document:
Article
Pays d'affiliation:
Chine