利用转录组测序数据的断点组装鉴定肺癌中的新型融合基因。
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.
作者信息
Fernandez-Cuesta Lynnette, Sun Ruping, Menon Roopika, George Julie, Lorenz Susanne, Meza-Zepeda Leonardo A, Peifer Martin, Plenker Dennis, Heuckmann Johannes M, Leenders Frauke, Zander Thomas, Dahmen Ilona, Koker Mirjam, Schöttle Jakob, Ullrich Roland T, Altmüller Janine, Becker Christian, Nürnberg Peter, Seidel Henrik, Böhm Diana, Göke Friederike, Ansén Sascha, Russell Prudence A, Wright Gavin M, Wainer Zoe, Solomon Benjamin, Petersen Iver, Clement Joachim H, Sänger Jörg, Brustugun Odd-Terje, Helland Åslaug, Solberg Steinar, Lund-Iversen Marius, Buettner Reinhard, Wolf Jürgen, Brambilla Elisabeth, Vingron Martin, Perner Sven, Haas Stefan A, Thomas Roman K
出版信息
Genome Biol. 2015 Jan 5;16(1):7. doi: 10.1186/s13059-014-0558-0.
Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline) (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondary rearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.
基因组易位事件常常通过产生具有致癌特性的基因融合体而成为癌症发展的基础。通过转录组测序鉴定此类融合转录本可能有助于发现新的潜在治疗靶点。我们开发了TRUP（适用于肿瘤样本的RNA测序统一流程）（https://github.com/ruping/TRUP），这是一种计算方法，它将分裂读段和读段对分析与从头组装相结合，用于鉴定癌症样本中的嵌合转录本。我们将TRUP应用于不同肿瘤类型的RNA测序数据，发现它在检测嵌合转录本方面比其他工具更敏感，例如EML4-ALK阳性肺肿瘤中的二次重排，或影响RASSF8的复发性失活重排。
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