Efficient epistasis inference via higher-order covariance matrix factorization.

IF 3.3 3区生物学 Q2 GENETICS & HEREDITY

Genetics Pub Date : 2025-06-20 DOI:10.1093/genetics/iyaf118

Kai S Shimagaki, John P Barton

引用次数: 0

Abstract

Epistasis can profoundly influence evolutionary dynamics. Temporal genetic data, consisting of sequences sampled repeatedly from a population over time, provides a unique resource to understand how epistasis shapes evolution. However, detecting epistatic interactions from sequence data is technically challenging. Existing methods for identifying epistasis are computationally demanding, limiting their applicability to real-world data. Here, we present a novel computational method for inferring epistasis that substantially reduces computational costs without sacrificing accuracy. We validated our approach in simulations and applied it to study HIV-1 evolution over multiple years in a data set of 16 individuals. There we observed a strong excess of negative epistatic interactions between beneficial mutations, especially mutations involved in immune escape. Our method is general and could be used to characterize epistasis in other large data sets.

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基于高阶协方差矩阵分解的上位推理。

上位性可以深刻地影响进化动力学。时间遗传数据，包括随时间从种群中反复采样的序列，为理解上位性如何影响进化提供了独特的资源。然而，从序列数据中检测上位性相互作用在技术上具有挑战性。现有的识别上位性的方法在计算上要求很高，限制了它们对现实世界数据的适用性。在这里，我们提出了一种新的计算方法来推断上位性，在不牺牲准确性的情况下大大降低了计算成本。我们在模拟中验证了我们的方法，并将其应用于研究HIV-1多年来在16个个体的数据集中的进化。在那里，我们观察到有益突变，特别是涉及免疫逃逸的突变之间的负上位相互作用的强烈过剩。我们的方法是通用的，可以用来描述其他大型数据集中的上位性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genetics GENETICS & HEREDITY-

CiteScore

6.90

自引率

6.10%

发文量

177

审稿时长

1.5 months

期刊介绍： GENETICS is published by the Genetics Society of America, a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work. While it has an illustrious history, GENETICS has changed along with the communities it serves: it is not your mentor''s journal. The editors make decisions quickly – in around 30 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is a peer reviewed, peer-edited journal, with an international reach and increasing visibility and impact. All editorial decisions are made through collaboration of at least two editors who are practicing scientists. GENETICS is constantly innovating: expanded types of content include Reviews, Commentary (current issues of interest to geneticists), Perspectives (historical), Primers (to introduce primary literature into the classroom), Toolbox Reviews, plus YeastBook, FlyBook, and WormBook (coming spring 2016). For particularly time-sensitive results, we publish Communications. As part of our mission to serve our communities, we''ve published thematic collections, including Genomic Selection, Multiparental Populations, Mouse Collaborative Cross, and the Genetics of Sex.