Evaluation of copy number variant detection from panel-based next-generation sequencing data
Evaluation of copy number variant detection from panel-based next-generation sequencing data
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DOI：
10.1002/mgg3.513
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发表时间：
2019-01-01
影响因子：
2
通讯作者：
Shen, Yiping
中科院分区：
文献类型：
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作者：
Yao, Ruen;Yu, Tingting;Shen, Yiping
背景靶向基因捕获和下一代测序(NGS)已被广泛用于检测一组疾病基因中的小变异，是一种可靠且经济有效的方法。拷贝数变异(CNV)也可以从阅读深度信息中推断出来，但从基于面板的NGS数据调用的CNV的准确性还没有得到很好的评估。方法对常规临床靶向平板测序的患者进行测序。以两个临床公认的平台，即染色体微阵列分析(CMA)和多连接依赖探针扩增(MLPA)产生的CNV为基准，对从靶向小组测序数据中检测到的致病CNV进行评估。在我们的研究中，CNVkit被用来使用阅读深度信息从测序数据中调用CNV。CMA和MLPA试验用于确认和进一步评估CNV的大小和断裂点。结果使用基于面板的NGS数据检测到的CNV大小超过300kb。使用NGS平台检测到的CNV大小略大于使用CMA平台(平均102.3%)，并且随着变体大小的增加，大小精度提高。使用NGS数据检测到的CNV断点与CMA检测到的断点非常接近(在2.3%的边际范围内)。然而，性染色体上的CNV在NGS和CMA平台之间不太一致。结论与使用CMA方法一样，利用靶向面板测序数据可以准确地检测覆盖常染色体足够外显子的拷贝数变异。从性染色体中检测到的CNV需要进一步的评估和验证。除了外显子水平的缺失/复制和性染色体上的CNV，我们的数据支持使用基于小组的NGS数据来常规临床检测致病CNV。
Background Targeted gene capture and next-generation sequencing (NGS) has been widely utilized as a robust and cost-effective approach for detecting small variants among a group of disease genes. Copy number variations (CNV) can also be inferred from the read-depth information but the accuracy of CNVs called from panel-based NGS data has not been well evaluated. Methods Sequencing data were acquired from patients underwent routine clinical targeted panel sequencing testing. Pathogenic CNVs detected from targeted panel sequencing data were evaluated using CNVs generated by two clinical accepted platforms, namely chromosome microarray analysis (CMA) and multiple ligation-dependent probe amplification (MLPA) as benchmarks. CNVkit was used in our study to call CNVs from sequencing data using read-depth information. CMA and MLPA tests were used to confirm and further assess the size and breakpoints of CNVs. Results The size of CNVs detected using panel-based NGS data are over 300 kb. The sizes of CNVs detected are slightly larger (102.3% on average) using the NGS platform than using the CMA platform, and the size accuracy improved as the size of variants increases. The breakpoints of CNVs detected using NGS data are quite close (within 2.3% of margin) to the breakpoints detected by CMA. CNVs on sex chromosomes, however, are less concordant between NGS and CMA platforms. Conclusion Copy number variations covering adequate exons on autosomes can be accurately detected using targeted panel sequencing data as using CMA. CNVs detected from sex chromosomes need further evaluation and validation. Except for exon-level deletion/duplication and CNV on sex chromosome, our data support the use of panel-based NGS data for routine clinical detection of pathogenic CNVs.