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在测序数据中忽视了质量差的患者样本,这会损害已发表的临床相关数据集的可重复性

Maximilian Sprang¹, Jannik Möllmann¹, Miguel A Andrade-Navarro²

¹Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany.

|August 16, 2024

概括

样本质量失衡显著影响基因表达研究,降低可复制性. 通过更好的实验设计和分析来解决这一问题,可以提高下游结果和科学可靠性.

科学领域:

生物医学研究的研究.
基因组学就是基因组学.
数据科学是数据科学.

背景情况:

在生物医学研究中,可复制性是一个关键问题,经常受到批量效应和样本质量失衡的阻碍.
目前的出版指南不充分解决样本质量变化,影响研究可靠性.
样本组之间的质量不平衡是影响研究可重复性的重要但被低估的因素.

研究的目的:

量化样本质量失衡对基因表达研究可重复性的影响.
为了确定与低质量的样本相关的常见生物效应.
评估质量失衡如何影响差异性基因表达分析和疾病相关基因的识别.

主要方法:

对40个临床相关的RNA测序 (RNA-seq) 数据集的分析.
质量失衡的量化及其与可重现度指标的相关性.
丰富分析用于识别低质量的样本中的生物途径和调节元素.
评估对差异性基因数量的影响以及质量和疾病基因在顶级结果中的比例.
根据质量分数测试异常值去除的效果.

主要成果:

在35%的分析数据集中观察到高质量失衡.
数以百计的质量标记在多个数据集中普遍存在,这表明了共同的潜在效应.
丰富分析表明,低质量的样本中存在压力驱动的影响,涉及转录因子和microRNAs.
质量失衡的增加与更多的差异基因和其中质量标志物的比例更高相关.
更高的质量失衡导致了已知疾病基因在顶部差异基因列表中的比例下降.
删除基于质量的异常值改善了下游分析结果.

结论:

样本组之间的质量失衡显著降低了差异性基因表达发现的相关性,从而降低了研究可重现性.
实施适当的实验设计和可靠的分析方法可以大大减轻质量失衡的负面影响.
这项研究强调了考虑和解决样本质量变异对于可靠的生物医学研究的重要性.

关键词:

生物信息学是一种生物信息学.在 ChIP-seqq.临床数据集临床数据集质量质量质量质量质量质量质量.质量标志物质量标志物质量标志物在RNA-seqqq.

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