FUSIM: a software tool for simulating fusion transcripts

BackgroundGene fusions are the result of chromosomal aberrations and encode chimeric RNA (fusion transcripts) that play an important role in cancer genesis. Recent advances in high throughput transcriptome sequencing have given rise to computational methods for new fusion discovery. The ability to simulate fusion transcripts is essential for testing and improving those tools.ResultsTo facilitate this need, we developed FUSIM (FUsion SIMulator), a software tool for simulating fusion transcripts. The simulation of events known to create fusion genes and their resulting chimeric proteins is supported, including inter-chromosome translocation, trans-splicing, complex chromosomal rearrangements, and transcriptional read through events.ConclusionsFUSIM provides the ability to assemble a dataset of fusion transcripts useful for testing and benchmarking applications in fusion gene discovery.

[1]  Krishna R. Kalari,et al.  A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines , 2011, Nucleic acids research.

[2]  Lee T. Sam,et al.  Transcriptome Sequencing to Detect Gene Fusions in Cancer , 2009, Nature.

[3]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[4]  J. Tchinda,et al.  Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. , 2006, Science.

[5]  B. Johansson,et al.  The impact of translocations and gene fusions on cancer causation , 2007, Nature Reviews Cancer.

[6]  T. Liehr,et al.  Complex chromosomal rearrangements: origin and meiotic behavior. , 2011, Human reproduction update.

[7]  Peter M. Rice,et al.  The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants , 2009, Nucleic acids research.

[8]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[9]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Sanghyuk Lee,et al.  ChimerDB 2.0—a knowledgebase for fusion genes updated , 2009, Nucleic Acids Res..

[11]  J. Rowley,et al.  Chromosome translocations: dangerous liaisons revisited , 2001, Nature Reviews Cancer.

[12]  Jian Ma,et al.  FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq , 2011, Bioinform..

[13]  H. Aburatani,et al.  Identification of the transforming EML4–ALK fusion gene in non-small-cell lung cancer , 2007, Nature.

[14]  Süleyman Cenk Sahinalp,et al.  deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data , 2011, PLoS Comput. Biol..

[15]  J. Tchinda,et al.  Recurrent Fusion of TMPRSS2 and ETS Transcription Factor Genes in Prostate Cancer , 2005, Science.

[16]  Leping Li,et al.  ART: a next-generation sequencing read simulator , 2012, Bioinform..

[17]  Christopher A. Maher,et al.  ChimeraScan: a tool for identifying chimeric transcription in sequencing data , 2011, Bioinform..

[18]  Song Liu,et al.  FUSIM: a software tool for simulating fusion , 2013 .

[19]  Fang Fang,et al.  FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution , 2011, Bioinform..