Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control
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DOI：
10.1093/bioinformatics/btaa751
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发表时间：
2021-04-01
期刊：
影响因子：
5.8
通讯作者：
Cai, James J.
中科院分区：
文献类型：
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作者：
Osorio, Daniel;Cai, James J.
动机：质量控制（QC）是单细胞RNA-seq （scRNA-seq）数据分析的关键步骤。在质量控制过程中，从分析中去除低质量的细胞，以避免对数据的误解。一个重要的质量控制指标是线粒体比例（mtDNA%），它被用作过滤掉低质量细胞的阈值。该领域的早期出版物将阈值设定为5%，从那时起，它就被用作scRNA-seq数据分析的几个软件包的默认值，并在许多scRNA-seq研究中被用作标准。然而，在不同物种、单细胞技术、组织和细胞类型之间使用统一阈值的有效性尚未得到充分评估。结果：我们系统地分析了PanglaoDB数据库中1349个带注释的数据集中报告的5 530 106个细胞，发现scRNA-seq数据中人类组织的平均mtDNA%显著高于小鼠组织。这种差异不受用于生成数据的平台的影响。基于这一发现，我们提出了121个小鼠组织和44个人类组织的mtDNA%的新参考值。一般来说，对于小鼠组织，5%的阈值可以很好地区分健康细胞和低质量细胞。然而，对于人体组织，5%的阈值应该重新考虑，因为它不能准确区分29.5%（44个组织中的13个）的健康细胞和低质量细胞。我们得出结论，省略mtDNA% QC过滤器或采用次优mtDNA%阈值可能导致对scRNA-seq数据的错误生物学解释。
Motivation: Quality control (QC) is a critical step in single-cell RNA-seq (scRNA-seq) data analysis. Low-quality cells are removed from the analysis during the QC process to avoid misinterpretation of the data. An important QC metric is the mitochondrial proportion (mtDNA%), which is used as a threshold to filter out low-quality cells. Early publications in the field established a threshold of 5% and since then, it has been used as a default in several software packages for scRNA-seq data analysis, and adopted as a standard in many scRNA-seq studies. However, the validity of using a uniform threshold across different species, single-cell technologies, tissues and cell types has not been adequately assessed.Results: We systematically analyzed 5 530 106 cells reported in 1349 annotated datasets available in the PanglaoDB database and found that the average mtDNA% in scRNA-seq data across human tissues is significantly higher than in mouse tissues. This difference is not confounded by the platform used to generate the data. Based on this finding, we propose new reference values of the mtDNA% for 121 tissues of mouse and 44 tissues of humans. In general, for mouse tissues, the 5% threshold performs well to distinguish between healthy and low-quality cells. However, for human tissues, the 5% threshold should be reconsidered as it fails to accurately discriminate between healthy and low-quality cells in 29.5% (13 of 44) tissues analyzed. We conclude that omitting the mtDNA% QC filter or adopting a suboptimal mtDNA% threshold may lead to erroneous biological interpretations of scRNA-seq data.