GenesisEgo, Seoul, Republic of Korea.
Department of Pharmacology, College of Medicine, Chung-Ang University, Seoul, Republic of Korea.
PLoS One. 2024 Nov 4;19(11):e0312203. doi: 10.1371/journal.pone.0312203. eCollection 2024.
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.
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.
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).
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.
随着公众对伴侣犬兴趣的增加，这些动物的健康问题也逐渐显现，因此需要优化全外显子组测序（WES）作为疾病预测的有价值方法。虽然针对人类基因组的 WES 已经得到很好的研究，但针对犬基因组的 WES 研究较少，需要找到有效的分析试剂盒。
我们比较和分析了 Twist 和 Agilent 的三种 WES 试剂盒在以犬基因组为目标的性能，以有效地进行犬病的基因分析。通过 Twist 和 Agilent 试剂盒的 WES，对来自 7 只未经任何干预的健康犬（3 只比格犬、1 只比雄犬、1 只马尔济斯犬、1 只威尔士柯基犬和 1 只混种犬）的犬基因组 DNA 样本的总读取量、重复率和变异调用水平进行了检测。
我们发现，虽然 Twist 的总读取数量最低，但 SSXT 系列的读取数量明显（P<0.05）更多。 Twist 的均匀度较低，标准差较高，但 SSXT 系列的均匀度相对较高。与 Twist 相比，SSXT 系列在深度为 30×时的目标比率显著（P<0.05）更高。在这四个试剂盒中，SSXT（O/N）的重复率最低（比 Twist 低 30%）。
试剂盒最重要的性能，即检测到的变异数量，Twist 为 48,302 个，SSXT（O/N）为 130,506 个。基于性能比较结果，发现 SSXT（O/N）的性能最好。
