Next-Generation Diagnostics: Gene Panel, Exome, or Whole Genome?
Next-Generation Diagnostics: Gene Panel, Exome, or Whole Genome?
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DOI：
10.1002/humu.22783
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发表时间：
2015-06-01
期刊：
影响因子：
3.9
通讯作者：
Santen, Gijs W. E.
中科院分区：
文献类型：
--
作者：
Sun, Yu;Ruivenkamp, Claudia A. L.;Santen, Gijs W. E.
尽管下一代测序（NGS）在诊断智力残疾（ID）等异质性疾病方面的优势是无可争议的，但对于靶向富集、全外显子组测序（WES）或全基因组测序（WGS）的相对优点几乎没有共识。为了回答这个问题，将来自相同9个样品的WES和WGS数据进行了比较，并且显示WES在包括与ID（500 GP）连锁的大约500个基因的基因组中没有错过WGS鉴定的任何变体。此外，深度测序的WES数据显示足以覆盖约99%的500 GP;因此，预期靶向富集方法几乎没有额外的益处。为了降低成本，通过研究测序读数与结果参数（例如覆盖率和变体产量）之间的关系来确定最低测序标准。我们的分析表明，6000万次读取产生的平均覆盖率约为60 x：500 GP序列中约97%被充分覆盖以排除变体，而变体产率约为99.5%，并且假阳性和假阴性率得到控制。我们的研究结果表明，WES是目前ID诊断的最佳方法。该结果取决于所使用的捕获试剂盒和测序策略。然而，所开发的框架适用于其他测序方法。
Although the benefits of next-generation sequencing (NGS) for the diagnosis of heterogeneous diseases such as intellectual disability (ID) are undisputed, there is little consensus on the relative merits of targeted enrichment, whole-exome sequencing (WES) or whole-genome sequencing (WGS). To answer this question, WES and WGS data from the same nine samples were compared, and WES was shown not to miss any variants identified by WGS in a gene panel including approximate to 500 genes linked to ID (500GP). Additionally, deeply sequenced WES data were shown to adequately cover approximate to 99% of the 500GP; thus, little additional benefit was to be expected from a targeted enrichment approach. To reduce costs, minimal sequencing criteria were determined by investigating the relation between sequenced reads and outcome parameters such as coverage and variant yield. Our analysis indicated that 60 million reads yielded a mean coverage of approximate to 60x: approximate to 97% of the 500GP sequences were sufficiently covered to exclude variants, whereas variant yield was approximate to 99.5% and false-positive and false-negative rates were controlled. Our findings indicate that WES is currently the optimal approach to ID diagnostics. This result depends on the capture kit and sequencing strategy used. The developed framework however is amenable to other sequencing approaches.