STANDARDIZE QC PROCEDURE FOR SCRNA-SEQ

IF 6.1 2区 医学 Q1 CLINICAL NEUROLOGY European Neuropsychopharmacology Pub Date : 2024-10-01 DOI:10.1016/j.euroneuro.2024.08.025
Shansha Peng , Chunyu Liu
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Abstract

Single-cell RNA sequencing (scRNA-seq) has emerged as a pivotal technology for dissecting cellular heterogeneity and function. In an effort to assess the consistency and rigor of quality control (QC) measures across scRNA-seq studies, we systematically reviewed publications from high-impact journals, including Cell, Nature, Science, and their major sister journals. Our analysis revealed a lack of standardization in QC procedures, with significant variability in the parameters employed. Despite general agreement on the necessity of certain QC steps, such as the removal of low-quality cells and the detection of doublets, the specific criteria for these steps were often arbitrarily defined and not universally applied. Notably, the assessment of ambient RNA contamination and the precision of gene expression measurements were frequently overlooked, potentially leading to the inclusion of spurious data in downstream analyses. To address these inconsistencies, we propose a revised set of QC procedures and parameters, which yielded distinct results compared to the original publications when applied to existing datasets. Moreover, we also assessed the performance of the existing data-driven QC tools in distinguishing the low-quality cells from the high-quality cells. Our findings underscore the urgent need for a standardized approach to QC in scRNA-seq to ensure the reliability and reproducibility of biological insights derived from this powerful technology.
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规范 SCNA SEQ 的 QC 程序
单细胞 RNA 测序(scRNA-seq)已成为剖析细胞异质性和功能的关键技术。为了评估scRNA-seq研究中质量控制(QC)措施的一致性和严谨性,我们系统地查阅了《细胞》、《自然》、《科学》等高影响力期刊及其主要姊妹期刊上发表的论文。我们的分析表明,质控程序缺乏标准化,所采用的参数差异很大。尽管大家普遍认为某些质控步骤是必要的,如去除低质量细胞和检测双顶体,但这些步骤的具体标准往往是随意定义的,并没有得到普遍应用。值得注意的是,对环境 RNA 污染和基因表达测量精度的评估经常被忽视,这可能导致下游分析中包含虚假数据。为了解决这些不一致的问题,我们提出了一套经过修订的质量控制程序和参数,在应用于现有数据集时,其结果与原始出版物的结果截然不同。此外,我们还评估了现有数据驱动质控工具在区分低质量细胞和高质量细胞方面的性能。我们的研究结果突出表明,迫切需要一种标准化的方法来对 scRNA-seq 进行质量控制,以确保从这项强大的技术中获得的生物学见解的可靠性和可重复性。
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来源期刊
European Neuropsychopharmacology
European Neuropsychopharmacology 医学-精神病学
CiteScore
10.30
自引率
5.40%
发文量
730
审稿时长
41 days
期刊介绍: European Neuropsychopharmacology is the official publication of the European College of Neuropsychopharmacology (ECNP). In accordance with the mission of the College, the journal focuses on clinical and basic science contributions that advance our understanding of brain function and human behaviour and enable translation into improved treatments and enhanced public health impact in psychiatry. Recent years have been characterized by exciting advances in basic knowledge and available experimental techniques in neuroscience and genomics. However, clinical translation of these findings has not been as rapid. The journal aims to narrow this gap by promoting findings that are expected to have a major impact on both our understanding of the biological bases of mental disorders and the development and improvement of treatments, ideally paving the way for prevention and recovery.
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