Joint detection of germline and somatic copy number events in matched tumor–normal sample pairs
Joint detection of germline and somatic copy number events in matched tumor–normal sample pairs
复制标题
联合检测匹配的肿瘤与正常样本对中的种系和体细胞拷贝数事件
DOI：
10.1093/bioinformatics/btz429
复制
发表时间：
2019
期刊：
影响因子：
5.8
通讯作者：
Yadong Wang
中科院分区：
文献类型：
--
作者：
Yongzhuang Liu;Jian Liu;Yadong Wang
动机肿瘤-正常样本对的全基因组测序 (WGS) 是一种在癌症研究和临床实践中全面表征种系拷贝数变异 (CNV) 和体细胞拷贝数改变 (SCNA) 的强大方法。现有的检测拷贝数事件的计算方法无法同时检测种系 CNV 和 SCNA，并且 SCNA 的准确性较低。结果在本研究中，我们开发了 TumorCNV，这是一种从匹配的肿瘤-正常样本对的 WGS 数据中联合检测种系 CNV 和 SCNA 的新方法。我们使用 COLO-829 黑色素瘤细胞系的模拟数据和真实数据，将 TumorCNV 与现有的拷贝数事件检测方法进行了比较。实验结果表明，TumorCNV 取得了比现有方法更优越的性能。可用性和实现软件 TumorCNV 是使用 Java 和 R 组合实现的，可以从网站 https://github.com/yongzhuang/TumorCNV 免费获取。补充信息补充数据可在 Bioinformaticsonline 上获得。
MotivationWhole-genome sequencing (WGS) of tumor–normal sample pairs is a powerful approach for comprehensively characterizing germline copy number variations (CNVs) and somatic copy number alterations (SCNAs) in cancer research and clinical practice. Existing computational approaches for detecting copy number events cannot detect germline CNVs and SCNAs simultaneously, and yield low accuracy for SCNAs.ResultsIn this study, we developed TumorCNV, a novel approach for jointly detecting germline CNVs and SCNAs from WGS data of the matched tumor–normal sample pair. We compared TumorCNV with existing copy number event detection approaches using the simulated data and real data for the COLO-829 melanoma cell line. The experimental results showed that TumorCNV achieved superior performance than existing approaches.Availability and implementationThe software TumorCNV is implemented using a combination of Java and R, and it is freely available from the website at https://github.com/yongzhuang/TumorCNV.Supplementary informationSupplementary data are available atBioinformaticsonline.