Division of Bioinformatics and Biostatistics, Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, Australia.
PLoS One. 2012;7(6):e39987. doi: 10.1371/journal.pone.0039987. Epub 2012 Jun 27.
The hallmarks of many haematological malignancies and solid tumours are chromosomal translocations, which may lead to gene fusions. Recently, next-generation sequencing techniques at the transcriptome level (RNA-Seq) have been used to verify known and discover novel transcribed gene fusions. We present FusionFinder, a Perl-based software designed to automate the discovery of candidate gene fusion partners from single-end (SE) or paired-end (PE) RNA-Seq read data. FusionFinder was applied to data from a previously published analysis of the K562 chronic myeloid leukaemia (CML) cell line. Using FusionFinder we successfully replicated the findings of this study and detected additional previously unreported fusion genes in their dataset, which were confirmed experimentally. These included two isoforms of a fusion involving the genes BRK1 and VHL, whose co-deletion has previously been associated with the prevalence and severity of renal-cell carcinoma. FusionFinder is made freely available for non-commercial use and can be downloaded from the project website (http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/).
许多血液恶性肿瘤和实体瘤的特征是染色体易位，这可能导致基因融合。最近，转录组水平（RNA-Seq）的下一代测序技术已被用于验证已知和发现新的转录基因融合。我们介绍了 FusionFinder，这是一个基于 Perl 的软件，旨在从单端（SE）或配对端（PE）RNA-Seq 读取数据中自动发现候选基因融合伙伴。FusionFinder 应用于先前发表的 K562 慢性髓性白血病（CML）细胞系分析的数据。使用 FusionFinder，我们成功复制了该研究的发现，并在其数据集中检测到了其他以前未报告的融合基因，这些基因已通过实验证实。其中包括涉及 BRK1 和 VHL 基因的融合的两种异构体，其共同缺失先前与肾细胞癌的普遍性和严重性相关。FusionFinder 可免费用于非商业用途，并可从项目网站（http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/）下载。
