Improvement of detection performance of fusion genes from RNA-seq data by clustering short reads
Improvement of detection performance of fusion genes from RNA-seq data by clustering short reads
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通过短读长聚类提高 RNA-seq 数据融合基因的检测性能
DOI：
10.1142/s0219720019400080
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发表时间：
2019
影响因子：
1
通讯作者：
Matsuda Hideo
中科院分区：
文献类型：
--
作者：
Sota Yoshiaki;Seno Shigeto;Shigeta Hironori;Osato Naoki;Shimoda Masafumi;Noguchi Shinzaburo;Matsuda Hideo
融合基因与癌症有关，在阅读长度相对较短的情况下，使用RNA-Seq检测它们是不够的。因此，我们提出了一种移位短读聚类(SSC)方法，该方法关注来自相同基因座的重叠阅读，并将其扩展为具有代表性的序列。为了验证它们的有效性，我们将SSC方法应用于四种类型的细胞系(BT-474、MCF-7、SKBR-3和T-47D)的RNA-Seq数据。当SSC方法的载玻片宽度增加到1、2、5或10个碱基时，读取长度分别从201个碱基延长到217(108%)、234(116%)、282(140%)或317(158%)个碱基。此外，使用融合基因检测工具STAR-Fusion在使用和不使用SSC方法的情况下对融合基因进行了研究。与原始数据相比，当SSC方法移动一个碱基时，定位到多个座位的读数从9.7%下降到4.6%，融合基因的敏感性从47%提高到54%(BT-474：从48%到57%，MCF-7：49%到53%，SKBR-3：50%到57%，T-47D：43%到50%)。当读数移动更多时，阳性预测值也会提高。SSC方法可能是一种有效的融合基因检测方法。
Fusion genes are involved in cancer, and their detection using RNA-Seq is insufficient given the relatively short reading length. Therefore, we proposed a shifted short-read clustering (SSC) method, which focuses on overlapping reads from the same loci and extends them as a representative sequence. To verify their usefulness, we applied the SSC method to RNA-Seq data from four types of cell lines (BT-474, MCF-7, SKBR-3, and T-47D). As the slide width of the SSC method increased to one, two, five, or ten bases, the read length was extended from 201 bases to 217 (108%), 234 (116%), 282 (140%), or 317 (158%) bases, respectively. Furthermore, fusion genes were investigated using STAR-Fusion, a fusion gene detection tool, with and without the SSC method. When one base was shifted by the SSC method, the reads mapped to multiple loci decreased from 9.7% to 4.6%, and the sensitivity of the fusion gene was improved from 47% to 54% on average (BT-474: from 48% to 57%, MCF-7: 49% to 53%, SKBR-3: 50% to 57%, and T-47D: 43% to 50%) compared with original data. When the reads are shifted more, the positive predictive value was also improved. The SSC method could be an effective method for fusion gene detection.