Ioncopy: a novel method for calling copy number alterations in amplicon sequencing data including significance assessment
Ioncopy: a novel method for calling copy number alterations in amplicon sequencing data including significance assessment
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DOI：
10.18632/oncotarget.7451
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发表时间：
2016-03-15
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影响因子：
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通讯作者：
Denkert, Carsten
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文献类型：
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作者：
Budczies, Jan;Pfarr, Nicole;Denkert, Carsten
最近，已经证明从扩增子测序（AS）数据中调用拷贝数改变（CNA）是可行的。然而，大多数方法需要非肿瘤（生殖系）DNA用于数据标准化。在这里，我们提出了CNA检测的方法Ioncopy，它不需要正常对照，并包括一个显着性评估为每个检测到的alteration.Ioncopy在184临床注释乳腺癌的队列进行了评估。总共检测到252个扩增，其中183个（72.6%）可以通过询问相同基因的额外扩增子的调用来验证。此外，共发现33个缺失，其中27个（81.8%）可以验证。分析16个最常扩增的基因，其中11个基因的验证率超过89%。前16个基因中的11个在扩增的肿瘤中显示出显著的过表达。89.5%的HER2扩增的肿瘤是GRB 7和STARD 3共扩增的，而68.4%的HER2扩增的肿瘤具有额外的MED1扩增。通过HER2外显子19、20和21中的扩增子测量的CNA之间的相关性很强（所有R> 0.93）。与HER2免疫组化结合原位杂交的金标准相比，基于AS的检测HER2扩增的灵敏度为90.0%，特异性为98.8%。使用Ioncopy，AS提供了一种简单有效的方法，可以在一次检测中同时分析基因扩增和基因缺失以及简单的体细胞突变。
Recently, it has been demonstrated that calling of copy number alterations (CNAs) from amplicon sequencing (AS) data is feasible. Most approaches, however, require non-tumor (germline) DNA for data normalization. Here, we present the method Ioncopy for CNA detection which requires no normal controls and includes a significance assessment for each detected alteration.Ioncopy was evaluated in a cohort of 184 clinically annotated breast carcinomas. A total number of 252 amplifications were detected, of which 183 (72.6%) could be validated by a call of an additional amplicon interrogating the same gene. Moreover, a total number of 33 deletions were found, whereof 27 (81.8%) could be validated. Analyzing the 16 most frequently amplified genes, validation rates of over 89% could be achieved for 11 of these genes. 11 of the top 16 genes showed significant overexpression in the amplified tumors. 89.5% of the HER2-amplified tumors were GRB7 and STARD3 co-amplified, whereas 68.4% of the HER2-amplified tumors had additional MED1 amplifications. Correlations between CNAs measured by amplicons in HER2 exons 19, 20 and 21 were strong (all R > 0.93). AS based detection of HER2 amplifications had a sensitivity of 90.0% and a specificity of 98.8% compared to the gold standard of HER2 immunohistochemistry combined with in situ hybridization.In summary, we developed and validated a novel method for detection and significance assessment of CNAs in amplicon sequencing data. Using Ioncopy, AS offers a straightforward and efficient approach to simultaneously analyze gene amplifications and gene deletions together with simple somatic mutations in a single assay.