Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs.
Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs.
复制标题
解决有害和近中性的影响需要不同的混合适应性检测设计。
DOI：
10.1007/s00239-023-10110-7
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发表时间：
2023
影响因子：
3.9
通讯作者：
Baym,Michael
中科院分区：
文献类型：
--
作者：
Limdi,Anurag;Baym,Michael
基于合并测序的适应性测定是一种强大且广泛使用的方法，用于并行量化数千种遗传变异的适应性。尽管这种测定的通量，它们倾向于在适应性估计中的偏差，并且相对于中性效应，对于有害的适应性效应，测量中的误差通常更大。在实践中，设计合并的适应性测定涉及时间点数量、测序深度和其他参数之间的权衡，以在可行的实验中获得尽可能多的信息。在这里，我们结合了模拟和重新分析现有的实验数据集，以探索如何使用标准的健身估计器的测定参数影响测量的近中性和有害的健身效果。我们发现，在相对适度的深度上对多个时间点进行排序可以改善对接近中性的健身效应的估计，但对有害效应的测量存在系统性偏差。我们发现，固定的读数总数，在更少的时间点进行更深的测序，提高了有害适应性效应的分辨率。我们的研究结果强调了一个固定量的数据的有害和近中性的影响大小的测量之间的权衡，并建议健身检测设计应调整健身效果，是相关的特定的生物问题。
Pooled sequencing-based fitness assays are a powerful and widely used approach to quantifying fitness of thousands of genetic variants in parallel. Despite the throughput of such assays, they are prone to biases in fitness estimates, and errors in measurements are typically larger for deleterious fitness effects, relative to neutral effects. In practice, designing pooled fitness assays involves tradeoffs between the number of timepoints, the sequencing depth, and other parameters to gain as much information as possible within a feasible experiment. Here, we combined simulations and reanalysis of an existing experimental dataset to explore how assay parameters impact measurements of near-neutral and deleterious fitness effects using a standard fitness estimator. We found that sequencing multiple timepoints at relatively modest depth improved estimates of near-neutral fitness effects, but systematically biased measurements of deleterious effects. We showed that a fixed total number of reads, deeper sequencing at fewer timepoints improved resolution of deleterious fitness effects. Our results highlight a tradeoff between measurement of deleterious and near-neutral effect sizes for a fixed amount of data and suggest that fitness assay design should be tuned for fitness effects that are relevant to the specific biological question.