TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
Top Cited Papers
Open Access
- 11 August 2011
- journal article
- method
- Published by Springer Nature in Genome Biology
- Vol. 12 (8) , 1-15
- https://doi.org/10.1186/gb-2011-12-8-r72
Abstract
TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/.Keywords
This publication has 27 references indexed in Scilit:
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiationNature Biotechnology, 2010
- Chimeric transcript discovery by paired-end transcriptome sequencingProceedings of the National Academy of Sciences, 2009
- Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell lineProceedings of the National Academy of Sciences, 2009
- Transcriptome sequencing to detect gene fusions in cancerNature, 2009
- A large genome center's improvements to the Illumina sequencing systemNature Methods, 2008
- Accurate whole human genome sequencing using reversible terminator chemistryNature, 2008
- Mapping and quantifying mammalian transcriptomes by RNA-SeqNature Methods, 2008
- Highly Integrated Single-Base Resolution Maps of the Epigenome in ArabidopsisCell, 2008
- Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer†Genes, Chromosomes and Cancer, 2002
- BLAT—The BLAST-Like Alignment ToolGenome Research, 2002