Smela Merrick Pierson, Pepe Valerio, Church George M
Wyss Institute at Harvard University, Cambridge, Massachusetts, United States of America.
Equal contributions.
bioRxiv. 2023 Oct 28:2023.09.27.559766. doi: 10.1101/2023.09.27.559766.
1Over 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, on-target and off-target editing errors, and microbial contamination can arise during PSC culture or due to undesired editing outcomes. Any of these abnormalities can invalidate experiments, so detecting them is crucial. The ongoing decline of next-generation sequencing prices has made whole genome sequencing (WGS) an effective quality control option, since WGS can detect any abnormality involving changes to DNA sequences or presence of unwanted sequences. However, this approach has suffered from 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 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.
在过去十年中，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PSC系，以研究各种各样的生物学问题。然而，在PSC培养过程中或由于不理想的编辑结果，可能会出现细胞系异常，如非整倍体、靶向和脱靶编辑错误以及微生物污染。这些异常中的任何一种都可能使实验无效，因此检测它们至关重要。下一代测序价格的持续下降使全基因组测序（WGS）成为一种有效的质量控制选择，因为WGS可以检测任何涉及DNA序列变化或不需要序列存在的异常。然而，这种方法一直缺乏易于使用的数据分析软件。在这里，我们介绍SeqVerify，这是一个计算流程，旨在获取原始WGS数据和预期编辑列表，并验证编辑是否存在以及是否没有异常。我们预计SeqVerify将成为生成经过编辑的PSC的研究人员的有用工具，更广泛地说，对于一般的细胞系质量控制也是如此。
