SeqVerify:细胞系基因组完整性、污染和基因编辑结果的便捷分析工具。

IF 5.9 2区 医学 Q1 CELL & TISSUE ENGINEERING
Stem Cell Reports Pub Date : 2024-10-08 Epub Date: 2024-09-12 DOI:10.1016/j.stemcr.2024.08.004
Merrick Pierson Smela, Valerio Pepe, Steven Lubbe, Evangelos Kiskinis, George M Church
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引用次数: 0

摘要

过去十年来,基因组编辑和多能干细胞(PSC)培养技术的进步使研究人员能够生成经过编辑的多能干细胞系,用于研究各种生物学问题。然而,在多能干细胞培养过程中或由于不希望出现的编辑结果,细胞系中可能会出现非整倍体、突变、靶上和非靶上编辑错误以及微生物污染等异常情况。随着下一代测序价格的不断下降,全基因组测序(WGS)已成为检测这些异常的一个很有前景的选择。然而,这种方法却因缺乏易于使用的数据分析软件而受阻。在这里,我们介绍 SeqVerify,它是一种计算管道,旨在获取原始 WGS 数据和预期基因组编辑列表,并验证编辑是否存在,以及是否存在异常。我们预计 SeqVerify 将成为研究人员生成编辑过的 PSCs 的有用工具,更广泛地说,它将成为细胞系质量控制的有用工具。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
SeqVerify: An accessible analysis tool for cell line genomic integrity, contamination, and gene editing outcomes.

Over the last decade, advances in genome editing and pluripotent stem cell (PSC) culture have let researchers generate edited PSC lines to study a wide variety of biological questions. However, abnormalities in cell lines such as aneuploidy, mutations, on-target and off-target editing errors, and microbial contamination can arise during PSC culture or due to undesired editing outcomes. The ongoing decline of next-generation sequencing prices has made whole-genome sequencing (WGS) a promising option for detecting these abnormalities. However, this approach has been held back by a lack of easily usable data analysis software. Here, we present SeqVerify, a computational pipeline designed to take raw WGS data and a list of intended genome edits, and verify that the edits are present and that there are no abnormalities. We anticipate that SeqVerify will be a useful tool for researchers generating edited PSCs, and more broadly, for cell line quality control in general.

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来源期刊
Stem Cell Reports
Stem Cell Reports CELL & TISSUE ENGINEERING-CELL BIOLOGY
CiteScore
10.50
自引率
1.70%
发文量
200
审稿时长
28 weeks
期刊介绍: Stem Cell Reports publishes high-quality, peer-reviewed research presenting conceptual or practical advances across the breadth of stem cell research and its applications to medicine. Our particular focus on shorter, single-point articles, timely publication, strong editorial decision-making and scientific input by leaders in the field and a "scoop protection" mechanism are reasons to submit your best papers.
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