系统地比较目标基因组测序的变异调用管道,跨越多个下一代测序器
Baosheng Feng1, Juan Lai1, Xue Fan2
1GeneMind Biosciences Company Limited, Shenzhen, China.
Frontiers in genetics
|January 19, 2024
概括
针对性基因组测序 (TS) 平台和生物信息学管道的基准测试对于精确瘤学至关重要. 配备SNVer和VarScan 2算法的FASTASeq 300平台在变种检测方面表现出卓越的灵敏度和速度.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 在瘤学瘤学.
背景情况:
- 针对性基因组测序 (TS) 对精确瘤学至关重要,它可以快速准确地检测遗传变异.
- 测序平台和变量调用工具的扩散给研究人员在选择最佳方法方面带来了挑战.
- 必须进行系统的基准测试研究,以指导选择有效的TS平台和生物信息学管道.
研究的目的:
- 为了对商业上可用的测序平台和生物信息学管道进行基因组测序的基准比较.
- 在不同平台和工具上评估测序质量,变异检测灵敏度和精度.
- 为最佳的TS策略提供建议,并为未来的研究确定新型变异基因.
主要方法:
- 在使用四台商用测序器和TSO500面板的参考OncoSpan FFPE样本上进行了定向基因组测序.
- 通过使用五个常见的生物信息学管道分析了50个结果数据集.
- 系统地调查测序质量指标 (基础质量,覆盖范围,深度) 和变异检测性能 (灵敏度,精度).
主要成果:
- 所有四个测序平台在基础质量 (Q20>94%) 覆盖率 (>97%) 和深度 (>2000×) 方面都表现出高一致性.
- 在使用SNVer和VarScan 2进行分析时,FASTASeq 300平台实现了100%的灵敏度和精度,用于高可靠性变体,测序时间最短 (∼21小时).
- 在各种样本类型中,SNVer和VarScan 2在SNP和InDel检测方面表现出卓越的性能,包括cfDNA和癌细胞系.
结论:
- 与SNVer和VarScan 2相结合的FASTASeq 300平台为敏感和高效的定向基因组测序提供了最佳的组合.
- 建议整合多个生物信息学工具,以提高变异调用准确度和灵敏度.
- 这项研究为对瘤TS的新协议和平台进行基准测试提供了宝贵的资源,并确定了癌症研究潜在的新型变异基因.
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