School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
Sci Rep. 2020 Feb 26;10(1):3501. doi: 10.1038/s41598-020-60559-5.
In the past decade, treatments for tumors have made remarkable progress, such as the successful clinical application of targeted therapies. Nowadays, targeted therapies are based primarily on the detection of mutations, and next-generation sequencing (NGS) plays an important role in relevant clinical research. The mutation frequency is a major problem in tumor mutation detection and increasing sequencing depth is a widely used method to improve mutation calling performance. Therefore, it is necessary to evaluate the effect of different sequencing depth and mutation frequency as well as mutation calling tools. In this study, Strelka2 and Mutect2 tools were used in detecting the performance of 30 combinations of sequencing depth and mutation frequency. Results showed that the precision rate kept greater than 95% in most of the samples. Generally, for higher mutation frequency (≥20%), sequencing depth ≥200X is sufficient for calling 95% mutations; for lower mutation frequency (≤10%), we recommend improving experimental method rather than increasing sequencing depth. Besides, according to our results, although Strelka2 and Mutect2 performed similarly, the former performed slightly better than the latter one at higher mutation frequency (≥20%), while Mutect2 performed better when the mutation frequency was lower than 10%. Besides, Strelka2 was 17 to 22 times faster than Mutect2 on average. Our research will provide a useful and comprehensive guideline for clinical genomic researches on somatic mutation identification through systematic performance comparison among different sequencing depths and mutation frequency.
在过去的十年中，肿瘤治疗取得了显著的进展，例如靶向治疗的成功临床应用。如今，靶向治疗主要基于突变的检测，而下一代测序（NGS）在相关的临床研究中起着重要作用。突变频率是肿瘤突变检测中的一个主要问题，增加测序深度是提高突变调用性能的一种常用方法。因此，有必要评估不同测序深度和突变频率以及突变调用工具的效果。在这项研究中，Strelka2 和 Mutect2 工具用于检测 30 种测序深度和突变频率组合的性能。结果表明，在大多数样本中，准确率保持在 95%以上。一般来说，对于较高的突变频率（≥20%），测序深度≥200X 足以调用 95%的突变；对于较低的突变频率（≤10%），我们建议改进实验方法而不是增加测序深度。此外，根据我们的结果，虽然 Strelka2 和 Mutect2 的性能相似，但前者在较高的突变频率（≥20%）下的性能略优于后者，而 Mutect2 在突变频率低于 10%时的性能更好。此外，Strelka2 的平均速度比 Mutect2 快 17 到 22 倍。我们的研究将通过对不同测序深度和突变频率的系统性能比较，为临床基因组学中体细胞突变识别提供有用且全面的指南。
