title: TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
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/.
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. infphilo@umiacs.umd.edu
authors.forename: Daehwan
authors.initials: D
authors.lastname: Kim
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001943:Breast Neoplasms / Q000378:metabolism; D045744:Cell Line, Tumor; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D050939:Gene Fusion; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D011471:Prostatic Neoplasms / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012984:Software