FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.
FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.
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DOI：
10.1186/1471-2105-14-193
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发表时间：
2013-06-15
影响因子：
3
通讯作者：
Zhou X
中科院分区：
文献类型：
--
作者：
Liu C;Ma J;Chang CJ;Zhou X
基因融合是由染色体异常重排引起的，是癌症发展的致病因素。新兴的RNA-Seq技术使我们能够检测基因融合并分析其特征。在本文中，我们提出了一种新的融合检测工具，FusionQ，基于双端RNA-Seq数据。该工具可以检测基因融合，构建嵌合体转录本的结构，并估计其丰度。为了确认融合点两侧的读段比对，我们采用了一种新的方法，“残留序列延伸”，其通过聚合读段的重叠读段来延伸读段的短片段。我们还提出了一个过滤器列表来控制假阳性率。此外，我们使用期望最大化算法估计融合丰度与稀疏优化，并进一步采用它来提高融合转录本的检测精度。利用FusionQ和另外两种先进的融合检测工具进行了仿真。FusionQ在灵敏度和特异性上都超过了其他两种，尤其是在低覆盖融合检测方面。使用来自乳腺癌细胞系的配对末端RNA-Seq数据，FusionQ检测到了先前报道的和新的融合。FusionQ报道了这些融合体的结构并提供了它们的表达。FusionQ检测到的一些高表达融合基因是乳腺癌中重要的生物标志物。与另外两种工具相比，FusionQ在取消线数据上的性能仍然显示出更好的特异性和灵敏度。FusionQ是一种基于RNA-Seq数据的融合检测和定量的新工具。它具有良好的特异性和敏感性。FusionQ是免费的，可在http://www.wakehealth.edu/CTSB/Software/Software.htm上获得。
Gene fusions, which result from abnormal chromosome rearrangements, are a pathogenic factor in cancer development. The emerging RNA-Seq technology enables us to detect gene fusions and profile their features. In this paper, we proposed a novel fusion detection tool, FusionQ, based on paired-end RNA-Seq data. This tool can detect gene fusions, construct the structures of chimerical transcripts, and estimate their abundances. To confirm the read alignment on both sides of a fusion point, we employed a new approach, “residual sequence extension”, which extended the short segments of the reads by aggregating their overlapping reads. We also proposed a list of filters to control the false-positive rate. In addition, we estimated fusion abundance using the Expectation-Maximization algorithm with sparse optimization, and further adopted it to improve the detection accuracy of the fusion transcripts. Simulation was performed by FusionQ and another two stated-of-art fusion detection tools. FusionQ exceeded the other two in both sensitivity and specificity, especially in low coverage fusion detection. Using paired-end RNA-Seq data from breast cancer cell lines, FusionQ detected both the previously reported and new fusions. FusionQ reported the structures of these fusions and provided their expressions. Some highly expressed fusion genes detected by FusionQ are important biomarkers in breast cancer. The performances of FusionQ on cancel line data still showed better specificity and sensitivity in the comparison with another two tools. FusionQ is a novel tool for fusion detection and quantification based on RNA-Seq data. It has both good specificity and sensitivity performance. FusionQ is free and available at http://www.wakehealth.edu/CTSB/Software/Software.htm.
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影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
3.7
作者：
Zhang LQ;Cheranova D;Gibson M;Ding S;Heruth DP;Fang D;Ye SQ
通讯作者：
Ye SQ
重复的DNA和下一代测序：计算挑战和解决方案。
DOI：
10.1038/nrg3117
发表时间：
2011-11-29
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
DOI：
10.1093/bioinformatics/btp692
发表时间：
2010-02-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li B;Ruotti V;Stewart RM;Thomson JA;Dewey CN
通讯作者：
Dewey CN
影响因子：
7
作者：
Li, Heng;Ruan, Jue;Durbin, Richard
通讯作者：
Durbin, Richard