The features of four kits for WES.

Objectives As the public’s interest in companion dogs grows, health issues in these animals are also emerging, necessitating the optimization of whole exome sequencing (WES) as a valuable method for disease prediction. While WES targeting the human genome is well established, WES targeting the canine genome is understudied, and there is a need to find effective analysis kits. Methods We compared and analyzed the performance of three WES kits from Twist and Agilent using the canine genome as the target to perform genetic analysis of canine diseases effectively. The levels of total reads, the duplication rate, and variant calling in canine genomic DNA samples from seven healthy dogs (three beagles, one bichon fry, one maltese, one welsh corgi, and one mixed breed) without any interventions were examined through WES via Twist and Agilent kits. Results We found that while Twist had the lowest total read number, the number of reads in the SSXT series was significantly (P<0.05) greater. Twist showed low evenness and high standard deviation, but the SSXT series showed relatively high evenness. Compared with Twist, the SSXT series from a depth of 30× presented a significantly (P<0.05) greater target ratio. Among the four kits, the significantly lowest duplicate ratio was confirmed for SSXT (O/N) (30% lower than Twist). Conclusion The most important performance of the kit, the number of variants detected, was 48,302 for Twist and 130,506 for SSXT (O/N). On the basis of the performance comparison results, SSXT (O/N) was found to have the best performance.一、研究目标 随着公众对伴侣犬的关注度日益提升，这类动物的健康问题也逐渐显现，亟需优化全外显子组测序（Whole Exome Sequencing，WES）技术，使其成为疾病预测的有效手段。目前针对人类基因组的WES技术已较为成熟，但针对犬类基因组的WES研究尚待深入，亟需开发有效的分析试剂盒。 二、研究方法 本研究以犬类基因组为靶标，对Twist与Agilent旗下的三款WES试剂盒的性能开展对比分析，以实现犬类疾病的高效遗传分析。我们选取7只未接受任何干预措施的健康犬（其中比格犬3只、比熊犬1只、马尔济斯犬1只、威尔士柯基犬1只、混血犬1只）的基因组DNA样本，通过Twist与Agilent试剂盒开展WES检测，对总reads数、重复率以及变异检出情况进行了分析。 三、研究结果 结果显示，尽管Twist试剂盒的总reads数最低，但其SSXT系列的reads数显著更高（P<0.05）。Twist试剂盒的测序均一性较低且标准差较高，而SSXT系列的测序均一性相对较高。与Twist试剂盒相比，在测序深度为30×时，SSXT系列的靶区域捕获比例显著更高（P<0.05）。四款试剂盒中，SSXT (O/N)的重复率显著最低，较Twist试剂盒低30%。 四、结论 本研究中衡量试剂盒核心性能的变异检出数指标显示，Twist试剂盒的检出数为48302，SSXT (O/N)试剂盒则为130506。基于上述性能对比结果，SSXT (O/N)试剂盒被证实为综合性能最优的产品。