Objective: The goal of this study was to compare the results of CNV detection by three different methods using 13 paired carcinoma samples, as well as to perform a statistical analysis of the agreement.Methods: CNV was studied using NanoString nCounter v2 Cancer CN Assay (Nanostring), Illumina Infinium CoreExome microarrays (CoreExome microarrays) and digital droplet PCR (ddPCR).Results: There was a good level of agreement (PABAK score > 0.6) between the CoreExome microarrays and the ddPCR results for finding CNVs. There was a moderate level of agreement (PABAK values ≈ 0.3–0.6) between the NanoString Assay results and microarrays or ddPCR. For 83 out of 87 target genes studied (95%), the agreement between the CoreExome microarrays and NanoString nCounter was characterized by PABAK values < 0.75, except for MAGI3, PDGFRA, NKX2-1 and KDR genes (>0.75). The MET, HMGA2, KDR, C8orf4, PAX9, CDK6, and CCND2 genes had the highest agreement among all three approaches.Conclusions: Therefore, to get a better idea of how to genotype an unknown CNV spectrum in tumor or normal tissue samples that are very different molecularly, it makes sense to use at least two CNV detection methods. One of them, like ddPCR, should be able to quantitatively confirm the results of the other.
目的：本研究旨在通过13对癌组织样本，比较三种不同方法检测拷贝数变异（CNV）的结果，并对检测结果的一致性进行统计分析。 方法：采用NanoString nCounter v2癌症CN检测试剂盒（Nanostring）、Illumina Infinium CoreExome微阵列芯片（CoreExome微阵列）和数字液滴PCR（ddPCR）三种技术进行CNV检测。 结果：CoreExome微阵列与ddPCR检测CNV结果具有良好的一致性（PABAK评分>0.6）。NanoString检测结果与微阵列或ddPCR结果之间呈现中等程度的一致性（PABAK值≈0.3–0.6）。在研究的87个靶基因中，有83个基因（95%）的CoreExome微阵列与NanoString nCounter检测一致性表现为PABAK值<0.75，仅MAGI3、PDGFRA、NKX2-1和KDR基因（>0.75）例外。MET、HMGA2、KDR、C8orf4、PAX9、CDK6和CCND2基因在三种检测方法中呈现最高的一致性。 结论：因此，为了更好地了解如何在分子特征差异显著的肿瘤或正常组织样本中对未知CNV谱进行基因分型，采用至少两种CNV检测方法是合理的。其中一种方法（如ddPCR）应能定量验证另一种方法的检测结果。
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