Reanalysis of RNA-Sequencing Data Reveals Several Additional Fusion Genes with Multiple Isoforms

Abstract

RNA-sequencing and tailored bioinformatic methodologies have paved the way for identification of expressed fusion genes from the chaotic genomes of solid tumors. We have recently successfully exploited RNA-sequencing for the discovery of 24 novel fusion genes in breast cancer. Here, we demonstrate the importance of continuous optimization of the bioinformatic methodology for this purpose, and report the discovery and experimental validation of 13 additional fusion genes from the same samples. Integration of copy number profiling with the RNA-sequencing results revealed that the majority of the gene fusions were promoter-donating events that occurred at copy number transition points or involved high-level DNA-amplifications. Sequencing of genomic fusion break points confirmed that DNA-level rearrangements underlie selected fusion transcripts. Furthermore, a significant portion (>60%) of the fusion genes were alternatively spliced. This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts.

RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas

“…1D; Sajan and Hawkins 2012). The ratio of intrachromosomal and interchromosomal translocations was consistent with those reported in breast cancer (Kangaspeska et al 2012).…”

InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data

“…Each study provides evidence for fusion genes that were first detected from RNA-seq data and then experimentally validated using RT-PCR or Sanger sequencing. Reanalysis of the Edgren et al dataset performed by Kangapeska et al [34] enabled detection and validation of an additional 13 fusion events, which we also included in our test. We assessed the performance of the analyzed tools by comparing the number of rediscovered known fusions and the total number of fusions reported by each algorithm.…”

“…Up to now, only TopHat-Fusion and ChimeraScan take the strand specificity provided by the library preparation protocol into account, but they do not mark whether a detected fusion was transcribed in the sense or antisense direction. Additionally, there is occasional evidence of functional fusion events with a breakpoint inside an exon [32] or involving non-coding [33], intronic [34, 35] or even intergenic regions [36]. Several studies have reported alternatively spliced isoforms of fusion genes [34, 37, 38].…”

“…Additionally, there is occasional evidence of functional fusion events with a breakpoint inside an exon [32] or involving non-coding [33], intronic [34, 35] or even intergenic regions [36]. Several studies have reported alternatively spliced isoforms of fusion genes [34, 37, 38]. Certain existing tools, including TopHat-Fusion, deFuse, SOAPfuse and fusionCatcher, are capable of detecting fusion isoforms.…”

Novel TNS3-MAP3K3 and ZFPM2-ELF5 fusion genes identified by RNA sequencing in multicystic mesothelioma with t(7;17)(p12;q23) and t(8;11)(q23;p13)

“…The quality of the raw sequence data was assessed using FastQC software (http://www.bioinformatics.babraham.ac.uk/ projects/fastqc/). Two softwares were used for the discovery of fusion transcripts: fusionmap/) [19] and FusionCatcher (version 0.99.3a beta-April 15, 2014) with the associated ENSEMBL, UCSC and RefSeq databases automatically downloaded by FusionCatcher (https://code.google.com/p/fusioncatcher/) [20]. FusionMap was run on a PC with Windows 7 professional as the operative system and FusionCatcher on a PC with Bio-Linux 7 as the operating system [21].…”