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全基因组长读测序下采样及其对变异调用精度和回忆的影响

William T Harvey¹, Peter Ebert^2,3,4, Jana Ebler^2,4

¹Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195-5065, USA.

Genome research

|January 8, 2024

概括

长读测序 (LRS) 提供了改进的基因组组装和变体检测. 牛津纳米孔技术 (ONT) 和太平洋生物科学 (PacBio) 的HiFi平台表现良好,PacBio HiFi在基于装配的变体调用方面表现出色.

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.
分子生物学分子生物学

背景情况:

长读测序 (LRS) 推进了全基因组测序,使新基因组分阶段组装和进入具有挑战性的基因组区域成为可能.
简单读取序列分析 (LRS) 能够更轻松地发现与疾病相关的复杂结构变异 (SV),超越了短读序列测序的限制.
尽管取得了进展,但LRS在成本,可扩展性和特定平台的读取精度方面面临挑战,需要仔细的实验设计.

研究的目的:

为了比较牛津纳米孔技术 (ONT) 和太平洋生物科学 (PacBio) HiFi平台的遗传变异调用精度和召回.
评估不同序列覆盖对LRS变种检测灵敏度和准确性的影响.
评估基因组组装对改进SV和indel变异调用使用LRS数据的好处.

主要方法:

在ONT和PacBio HiFi平台之间对变种呼叫性能进行比较分析.
序列覆盖水平的系统变化,以确定LRS应用的最佳值.
对基于读取和基于组装的变量调用集的F1分数的评估,以测量精度和回忆.

主要成果:

对于基于读取的应用程序,LRS的灵敏度高原约为12倍的覆盖率,大多数变体被准确地调用 (F1得分>0.5).
在结构变异检测方面,ONT和PacBio HiFi平台都表现出强大的性能.
基因组装增强了SV和indel的变体调用精度和回忆,PacBio HiFi在基于组装的变体调用中表现优于ONT.

结论:

对于LRS来说,可以设计出具有成本效益的实验策略,而不会影响发现新的生物见解.
在基因组组装质量和随后的变异调用方面,PacBio HiFi在ONT上表现出了优势.
随着LRS技术的不断发展,基因组分析的进一步改进有望实现.

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