Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.
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DOI：
10.1186/s12918-014-0097-z
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发表时间：
2014-09-04
影响因子：
--
通讯作者：
Rabadan R
中科院分区：
文献类型：
--
作者：
Abate F;Zairis S;Ficarra E;Acquaviva A;Wiggins CH;Frattini V;Lasorella A;Iavarone A;Inghirami G;Rabadan R
伊马替尼在治疗 BCR-ABL1 相关癌症方面取得的巨大成功强调了识别癌症中新型功能基因融合的必要性。 RNA 测序提供了表达转录本的全基因组视图，揭示了具有生物学功能的基因融合。尽管已经有几种生物信息学工具可用于检测假定的融合转录本，但候选事件列表受到非功能性通读事件、逆转录酶模板切换事件、不正确的映射和其他系统错误的困扰。此类列表缺乏任何致癌相关性的迹象，而且它们太大，无法进行详尽的实验验证。我们设计并实现了一个管道 Pegasus，用于注释和预测具有生物功能的基因融合候选者。 Pegasus 为各种基因融合检测工具、新型融合蛋白的重建、保留/丢失功能域的阅读框感知注释以及致癌潜力的数据驱动分类提供了通用接口。 Pegasus 极大地简化了致癌基因融合的搜索，弥合了原始 RNA-Seq 数据与最终易于处理的实验验证候选者列表之间的差距。我们展示了 Pegasus 在 176 个多形性胶质母细胞瘤 (GBM) 和 23 个间变性大细胞淋巴瘤 (ALCL) 病例的 RNA-Seq 样本中预测新驱动融合的有效性。联系方式：fa2306@columbia.edu。
The extraordinary success of imatinib in the treatment of BCR-ABL1 associated cancers underscores the need to identify novel functional gene fusions in cancer. RNA sequencing offers a genome-wide view of expressed transcripts, uncovering biologically functional gene fusions. Although several bioinformatics tools are already available for the detection of putative fusion transcripts, candidate event lists are plagued with non-functional read-through events, reverse transcriptase template switching events, incorrect mapping, and other systematic errors. Such lists lack any indication of oncogenic relevance, and they are too large for exhaustive experimental validation. We have designed and implemented a pipeline, Pegasus, for the annotation and prediction of biologically functional gene fusion candidates. Pegasus provides a common interface for various gene fusion detection tools, reconstruction of novel fusion proteins, reading-frame-aware annotation of preserved/lost functional domains, and data-driven classification of oncogenic potential. Pegasus dramatically streamlines the search for oncogenic gene fusions, bridging the gap between raw RNA-Seq data and a final, tractable list of candidates for experimental validation. We show the effectiveness of Pegasus in predicting new driver fusions in 176 RNA-Seq samples of glioblastoma multiforme (GBM) and 23 cases of anaplastic large cell lymphoma (ALCL). Contact: fa2306@columbia.edu.
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影响因子：
14.9
作者：
Kim P;Yoon S;Kim N;Lee S;Ko M;Lee H;Kang H;Kim J;Lee S
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Lee S
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作者：
Shugay, Mikhail;Ortiz de Mendibil, Inigo;Novo, Francisco J.
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Novo, Francisco J.
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Caride, Ariel
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通讯作者：
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作者：
Carrara, Matteo;Beccuti, Marco;Calogero, Raffaele A.
通讯作者：
Calogero, Raffaele A.