Determining the accuracy of next generation sequencing based copy number variation analysis in Hereditary Breast and Ovarian Cancer

Copy number variations (CNVs) are commonly associated with malignancies, including hereditary breast and ovarian cancers. Next generation sequencing (NGS) provides solutions for CNV detection in a single run. This study aimed to compare the accuracy of CNV detection by NGS analyzing tool against Multiplex Ligation Dependent Probe Amplification (MLPA).
In total, 1276 cases were studied by targeted NGS panels and 691 cases (61 calls in 58 NGS-CNV positive and 633 NGS-CNV negative cases) were validated by MLPA.
Twenty-eight (46%) NGS-CNV positive calls were consistent, whereas 33 (54%) calls showed discordance with MLPA. Two cases were detected as SNV by the NGS and CNV by the MLPA analysis. In total, 2% of the cases showed an MLPA confirmed CNV region in BRCA1/2. The results of this study showed that despite the high false positive call rate of the NGS-CNV algorithm, there were no false negative calls. The cases that were determined to be negative by the NGS and positive by the MLPA were actually carrying SNVs that were located on the MLPA probe binding sites.
The diagnostic performance of NGS-CNV analysis is promising; however, the need for confirmation by different methods remains.

拷贝数变异（Copy number variations, CNVs）通常与包括遗传性乳腺癌和卵巢癌在内的恶性肿瘤密切相关。下一代测序（Next generation sequencing, NGS）可在单次实验中完成拷贝数变异的检测。本研究旨在对比NGS分析工具与多重连接依赖式探针扩增（Multiplex Ligation Dependent Probe Amplification, MLPA）在CNV检测中的准确性。
本研究共纳入1276例接受靶向NGS测序Panel检测的样本，其中691例（含58例NGS检测为CNV阳性的样本中的61个变异检出结果，以及633例NGS检测为CNV阴性的样本）通过MLPA进行验证。其中28个（占比46%）NGS检出的CNV阳性结果与MLPA验证结果一致，另有33个（占比54%）结果与MLPA验证不符。另有2例样本经NGS检测被判定为单核苷酸变异（Single Nucleotide Variant, SNV）阳性，而MLPA分析则检出其存在CNV。总体而言，有2%的样本经MLPA验证存在BRCA1/2基因区域的拷贝数变异。
本研究结果显示，尽管NGS-CNV检测算法存在较高的假阳性检出率，但未出现假阴性结果。经NGS判定为阴性但MLPA检测为阳性的样本，实则携带位于MLPA探针结合位点上的单核苷酸变异。
NGS-CNV检测的诊断性能表现可观，但仍需通过其他检测方法进行结果验证。