Next-generation sequencing technology is developing rapidly and target capture sequencing has become an important technique. Several different platforms for library preparation and target capture with different bait types respectively are commercially available. Here we compare the performance of the four platforms with different bait types to find out their advantages and limitations. The purpose of this study is to help investigators and clinicians select the appropriate platform for their particular application and lay the foundation for the development of a better target capture platform for next-generation sequencing. We formulate capture efficiency as a novel parameter that can be used to better evaluations of specificity and coverage depth among the different capture platforms. Target coverage, capture efficiency, GC bias, AT Dropout, sensitivity in single nucleotide polymorphisms, small insertions and deletions detection, and the feature of each platform were compared for low input samples. In general, all platforms perform well and small differences among them are revealed. In our results, RNA baits have stronger binding power than DNA baits, and with ultra deep sequencing, double stranded RNA baits perform better than single stranded RNA baits in all aspects. DNA baits got better performance in the region with high GC content and RNA baits got lower AT dropout suggesting that the binding power is different between DNA and RNA baits to genome regions with different characteristics. The platforms with double stranded RNA baits have the most balanced capture performance. Our results show the key differences in performance among the four updated platforms with four different bait types. The better performance of double stranded RNA bait with ultra deep sequencing suggests that it may improve the sensitivity of ultra low frequent mutation detection. In addition, we further propose that the mixed baits of double stranded RNA and single stranded DNA may improve target capture performance.

中文翻译：

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四种外显子组 DNA 测序靶标富集诱饵的性能比较

新一代测序技术正在快速发展，靶标捕获测序已成为一项重要技术。市场上有几种不同的平台，分别用于不同诱饵类型的文库制备和目标捕获。在这里，我们比较了四个平台与不同诱饵类型的性能，以找出它们的优点和局限性。本研究的目的是帮助研究人员和临床医生为其特定应用选择合适的平台，并为开发更好的下一代测序目标捕获平台奠定基础。我们将捕获效率制定为一个新颖的参数，可用于更好地评估不同捕获平台之间的特异性和覆盖深度。针对低输入样品，比较了目标覆盖率、捕获效率、GC 偏差、AT Dropout、单核苷酸多态性的灵敏度、小插入和缺失检测以及每个平台的特征。总的来说，所有平台都表现良好，并且显示出它们之间的细微差异。在我们的结果中，RNA 诱饵比 DNA 诱饵具有更强的结合力，并且通过超深度测序，双链 RNA 诱饵在各方面都比单链 RNA 诱饵表现更好。DNA诱饵在GC含量高的区域中表现更好，RNA诱饵的AT丢失率较低，这表明DNA和RNA诱饵对具有不同特征的基因组区域的结合力不同。采用双链RNA诱饵的平台具有最平衡的捕获性能。我们的结果显示了具有四种不同诱饵类型的四个更新平台之间性能的主要差异。双链RNA诱饵与超深度测序的更好性能表明它可以提高超低频率突变检测的灵敏度。此外，我们进一步提出双链RNA和单链DNA的混合诱饵可以提高目标捕获性能。