Ploidy inference from single-cell data: application to human and mouse cell atlases.

IF 3.3 3区生物学

Genetics Pub Date : 2024-04-23 DOI:10.1093/genetics/iyae061

Fumihiko Takeuchi, Norihiro Kato

引用次数: 0

Abstract

Ploidy is relevant to numerous biological phenomena, including development, metabolism, and tissue regeneration. Single-cell RNA-seq and other omics studies are revolutionizing our understanding of biology, yet they have largely overlooked ploidy. This is likely due to the additional assay step required for ploidy measurement. Here, we developed a statistical method to infer ploidy from single-cell ATAC-seq data, addressing this gap. When applied to data from human and mouse cell atlases, our method enabled systematic detection of polyploidy across diverse cell types. This method allows for the integration of ploidy analysis into single-cell studies. Additionally, this method can be adapted to detect the proliferating stage in the cell cycle and copy number variations in cancer cells. The software is implemented as the scPloidy package of the R software and is freely available from CRAN.

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从单细胞数据推断倍性：应用于人类和小鼠细胞图谱。

倍性与许多生物现象有关，包括发育、新陈代谢和组织再生。单细胞RNA-seq和其他omics研究正在彻底改变我们对生物学的理解，但它们在很大程度上忽略了倍性。这可能是由于倍性测量需要额外的检测步骤。在这里，我们开发了一种从单细胞 ATAC-seq 数据推断倍性的统计方法，弥补了这一空白。当应用到人类和小鼠细胞图谱的数据时，我们的方法能够系统地检测不同细胞类型的多倍体。这种方法可将多倍体分析整合到单细胞研究中。此外，这种方法还可用于检测细胞周期的增殖阶段和癌细胞的拷贝数变化。该软件作为 R 软件的 scPloidy 软件包实现，可从 CRAN 免费获取。

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 生物-遗传学

CiteScore

6.20

自引率

6.10%

发文量

177

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.