MOTIVATION: Fusion transcripts can be created as a result of genome rearrangement in cancer. Some of them play important roles in carcinogenesis, and can serve as diagnostic and therapeutic targets. With more and more cancer genomes being sequenced by next-generation sequencing technologies, we believe an efficient tool for reliably identifying fusion transcripts will be desirable for many groups. RESULTS: We designed and implemented an open-source software tool, called FusionHunter, which reliably identifies fusion transcripts from transcriptional analysis of paired-end RNA-seq. We show that FusionHunter can accurately detect fusions that were previously confirmed by RT-PCR in a publicly available dataset. The purpose of FusionHunter is to identify potential fusions with high sensitivity and specificity and to guide further functional validation in the laboratory. AVAILABILITY: http://bioen-compbio.bioen.illinois.edu/FusionHunter/.
MOTIVATION: Fusion transcripts can be created as a result of genome rearrangement in cancer. Some of them play important roles in carcinogenesis, and can serve as diagnostic and therapeutic targets. With more and more cancer genomes being sequenced by next-generation sequencing technologies, we believe an efficient tool for reliably identifying fusion transcripts will be desirable for many groups. RESULTS: We designed and implemented an open-source software tool, called FusionHunter, which reliably identifies fusion transcripts from transcriptional analysis of paired-end RNA-seq. We show that FusionHunter can accurately detect fusions that were previously confirmed by RT-PCR in a publicly available dataset. The purpose of FusionHunter is to identify potential fusions with high sensitivity and specificity and to guide further functional validation in the laboratory. AVAILABILITY: http://bioen-compbio.bioen.illinois.edu/FusionHunter/.
Authors: John A Martignetti; Olga Camacho-Vanegas; Nolan Priedigkeit; Catalina Camacho; Elena Pereira; Li Lin; Leopold Garnar-Wortzel; Dagny Miller; Bojan Losic; Hardik Shah; Jun Liao; Jian Ma; Pratik Lahiri; Mark Chee; Eric Schadt; Peter Dottino Journal: Neoplasia Date: 2014-01 Impact factor: 5.715
Authors: Richard Meier; Stefan Graw; Peter Beyerlein; Devin Koestler; Julian R Molina; Jeremy Chien Journal: Nucleic Acids Res Date: 2017-05-19 Impact factor: 16.971
Authors: Genevieve C Kendall; Sarah Watson; Lin Xu; Collette A LaVigne; Whitney Murchison; Dinesh Rakheja; Stephen X Skapek; Franck Tirode; Olivier Delattre; James F Amatruda Journal: Elife Date: 2018-06-05 Impact factor: 8.140
Authors: Rocco Piazza; Alessandra Pirola; Roberta Spinelli; Simona Valletta; Sara Redaelli; Vera Magistroni; Carlo Gambacorti-Passerini Journal: Nucleic Acids Res Date: 2012-05-08 Impact factor: 16.971