SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads

Abstract

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.

Characterization of fusion genes in common and rare epithelial ovarian cancer histologic subtypes

“…Studies have underscored limitations associated with relying on any one fusion caller to detect fusions [ 19 – 21 ], therefore, we further examined whether the fusions in Table 1 were also detected by the robust fusion caller SoapFuse [ 22 ]. Five recurrent fusions detected by PRADA were also detected by SoapFuse (see Table 1 ).…”

“…Fusion events identified by PRADA in 17 (7 Mayo Clinic, 10 GTEx Portal) normal tissues were removed. A catalog of 11,531 fusion RNAs identified in over 200 RNA sequencing libraries from 27 different non-neoplastic human tissues analyzed using the SoapFuse pipeline was further used to remove fusion genes that are not cancer-specific [ 22 , 23 ]. To assess robustness of fusion results from PRADA pipeline, we also ran a subset of sample through three other fusion callers (SoapFuse, FusionMap and TopHat Fusion) with results presented in Supplementary Table 1 .…”

RNA‐Seq methods for transcriptome analysis

“…Created by chromosomal rearrangements, gene fusions are present in approximately 20% of cancer . Fusion events can be detected using RNA‐Seq data along with specific bioinformatic methods . Detection of a fusion event is typically revealed by reads containing fusion junctions or by differences in expression between the 5′ and 3′ ends of genes that are fused.…”

De Novo Transcriptome Sequencing of the Deep-Sea-Derived Fungus Dichotomomyces cejpii and Analysis of Gliotoxin Biosynthesis Genes

“…Then, CDS (coding domain sequences) were extracted based on BLAST results and then translated into peptide sequences. Moreover, BLAST result information was also used to train ESTScan [ 28 ]. The CDS of unigenes that had no hit in BLAST were predicted by ESTScan and then translated into peptide sequences.…”