Transcriptome Sequencing for the Detection of Chimeric Transcripts

The occurrence of chimeric transcripts has been reported in many cancer cells and seen as potential biomarkers and therapeutic targets. Modern high-throughput sequencing technologies offer a way to investigate individual chimeric transcripts and the systematic information of associated gene expressions about underlying genome structural variations and genomic interactions. Both assembly-based and alignment-based methods are used for the investigation of chimeric transcripts.

rna-seq

The basic workflow for the detection of chimeric transcripts

The expression of transcripts in a cell is dynamic. Next-generation sequencing is rapidly becoming the method of choice for the exploration of gene expressions. Furthermore, unlike hybridization-based detection, RNA -Seq allows genome-wide analysis of transcription at single-nucleotide resolution, including identification of including alternative splicing sites, posttranscriptional modifications, and fusion genes. As of 2015, the three most widely used NGS platforms for RNA-Seq are SOLiD and Ion Torrent and Illumina. Most of the RNA-Seq experiments use Illumina paired-end sequencing that allows users to sequence both ends of a fragment and generate high-fidelity reads. For the reason, most of published methods majorly deal with Illumina RNA-Seq data for finding chimeric transcript.

Fusion finding and de novo assembly programs for RNA -Seq analysis

Name

Source

References

Fusion finding algorithms

BreakDancer

http://​breakdancer.​sourceforge.​net/​

Fan et al. [15]

FusionSeq

http://​archive.​gersteinlab.​org/​proj/​rnaseq/​fusionseq/​

Sboner et al. [16]

MapSplice

http://​www.​netlab.​uky.​edu/​p/​bioinfo/​MapSplice

Wang et al. [17]

Tophat-fusion

http://ccb.jhu.edu.ezproxyhost.library.tmc.edu/software/tophat/fusion_ index.html

Kim et al. [10]

deFuse

https://​sourceforge.​net/​projects/​soapfuse/​

McPherson et al. [18]

FusionHunter

http://​bioen-compbio.​bioen.​illinois.​edu/​FusionHunter/​

Li et al. [19]

SnowShoes-FTD

http://​bioinformaticsto​ols.​mayo.​edu/​research/​snowshoes-ftd/​

Yan et al. [20]

ChimeraScan

https://​code.​google.​com/​p/​chimerascan/​

Iyer et al. [21]

FusionMap

http://​www.​arrayserver.​com/​wiki/​index.​php?​title=​FusionMap

Ge et al. [14]

FusionFinder

http://bioinformatics .childhealthresearch.org.au/software/fusionfinder/

Francis et al. [22]

FusionAnalyser

http://​www.​ngsbicocca.​org/​html/​fusionanalyser.​html

Piazza et al. [23]

SAOPfusion

http://​soap.​genomics.​org.​cn/​SOAPfusion.​html

Wu et al. [24]

SAOPfuse

http://​soap.​genomics.​org.​cn/​soapfuse.​html

Jia et al. [25]

FusionCatcher

https://​code.​google.​com/​p/​fusioncatcher/​

Nicorici et al. [13]

ViralFusionSeq

https://​sourceforge.​net/​projects/​viralfusionseq/​

Li et al. [26]

PRADA

http://bioinformatics .mdanderson.org/main/PRADA:Overview

Torres-Garcia et al. [27]

Chimera

http:///bioconductor.org/packages/release/bioc/html/chimera. html

Beccuti et al. [28]

TRUP

https://​github.​com/​ruping/​TRUP

Fernandez et al. [29]

De novo assembly algorithms

EBARDenovo

https://​sourceforge.​net/​projects/​ebardenovo/​

Chu et al. [8]

Trinity

http://​trinityrnaseq.​sourceforge.​net/​

Grabherr et al. [30]

Trans-ABySS

http://​www.​bcgsc.​ca/​platform/​bioinfo/​software/​trans-abyss

Robertson et al. [31]

Oases

https://​www.​ebi.​ac.​uk/​~zerbino/​oases/​

Schulz et al. [32]

An updated list of RNA -Seq tools is maintained at http://fusion _gene.aiplab.net/index.php/Tools

Chu HT. (2015) Transcriptome Sequencing for the Detection of Chimeric Transcripts. Methods Mol Biol 1381:239-53. [abstract]

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