Chilamakuri Chandra Sekhar Reddy, Lorenz Susanne, Madoui Mohammed-Amin, Vodák Daniel, Sun Jinchang, Hovig Eivind, Myklebost Ola, Meza-Zepeda Leonardo A
Department of Tumor Biology, Oslo University Hospital, Norwegian Radium Hospital, 0310 Oslo, Norway.
BMC Genomics. 2014 Jun 9;15(1):449. doi: 10.1186/1471-2164-15-449.
Recent developments in deep (next-generation) sequencing technologies are significantly impacting medical research. The global analysis of protein coding regions in genomes of interest by whole exome sequencing is a widely used application. Many technologies for exome capture are commercially available; here we compare the performance of four of them: NimbleGen's SeqCap EZ v3.0, Agilent's SureSelect v4.0, Illumina's TruSeq Exome, and Illumina's Nextera Exome, all applied to the same human tumor DNA sample.
Each capture technology was evaluated for its coverage of different exome databases, target coverage efficiency, GC bias, sensitivity in single nucleotide variant detection, sensitivity in small indel detection, and technical reproducibility. In general, all technologies performed well; however, our data demonstrated small, but consistent differences between the four capture technologies. Illumina technologies cover more bases in coding and untranslated regions. Furthermore, whereas most of the technologies provide reduced coverage in regions with low or high GC content, the Nextera technology tends to bias towards target regions with high GC content.
We show key differences in performance between the four technologies. Our data should help researchers who are planning exome sequencing to select appropriate exome capture technology for their particular application.
深度（新一代）测序技术的最新进展正在对医学研究产生重大影响。通过全外显子组测序对感兴趣的基因组中的蛋白质编码区域进行全局分析是一种广泛应用的方法。许多外显子组捕获技术都有商业产品；在这里，我们比较其中四种技术的性能：NimbleGen的SeqCap EZ v3.0、安捷伦的SureSelect v4.0、Illumina的TruSeq Exome和Illumina的Nextera Exome，所有这些技术都应用于同一个人类肿瘤DNA样本。
对每种捕获技术的不同外显子组数据库覆盖范围、目标覆盖效率、GC偏差、单核苷酸变异检测灵敏度、小插入缺失检测灵敏度和技术重复性进行了评估。总体而言，所有技术表现良好；然而，我们的数据表明这四种捕获技术之间存在微小但一致的差异。Illumina技术在编码区和非翻译区覆盖更多碱基。此外，虽然大多数技术在GC含量低或高的区域覆盖减少，但Nextera技术倾向于偏向GC含量高的目标区域。
我们展示了这四种技术在性能上的关键差异。我们的数据应该有助于计划进行外显子组测序的研究人员为其特定应用选择合适的外显子组捕获技术。
