Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes
Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes
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DOI：
10.1038/s41592-020-0820-1
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发表时间：
2020-05-04
期刊：
影响因子：
48
通讯作者：
Lawniczak, Mara K. N.
中科院分区：
文献类型：
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作者：
Heaton, Haynes;Talman, Arthur M.;Lawniczak, Mara K. N.
Souporcell利用基因型信息对单细胞RNA-seq数据进行聚类，无需使用基因型参考。对于包含不同基因型混合的样本，无论是自然混合还是实验混合，对单细胞RNA测序（scRNA-seq）数据进行解卷积的方法都是必要的。跨供体复用是一种流行的实验设计，它可以避免批次效应、降低成本并提高双细胞检测能力。通过利用在scRNA-seq读段中检测到的变异，可以将细胞归到其来源供体，并识别可能具有高度相似转录图谱的跨基因型双细胞，这些双细胞无法通过转录图谱检测到。更细微的跨基因型变异污染可用于估计环境RNA的量。环境RNA是由液滴分配前的细胞裂解导致的，是scRNA-seq分析的一个重要混杂因素。在此我们开发了souporcell，一种利用在scRNA-seq读段内检测到的基因变异对细胞进行聚类的方法。我们表明，它在基因型聚类、双细胞检测和环境RNA估计方面都达到了高精度，这在一系列具有挑战性的场景中都得到了证明。
Souporcell clusters single-cell RNA-seq data using genotype information without the use of a genotype reference.Methods to deconvolve single-cell RNA-sequencing (scRNA-seq) data are necessary for samples containing a mixture of genotypes, whether they are natural or experimentally combined. Multiplexing across donors is a popular experimental design that can avoid batch effects, reduce costs and improve doublet detection. By using variants detected in scRNA-seq reads, it is possible to assign cells to their donor of origin and identify cross-genotype doublets that may have highly similar transcriptional profiles, precluding detection by transcriptional profile. More subtle cross-genotype variant contamination can be used to estimate the amount of ambient RNA. Ambient RNA is caused by cell lysis before droplet partitioning and is an important confounder of scRNA-seq analysis. Here we develop souporcell, a method to cluster cells using the genetic variants detected within the scRNA-seq reads. We show that it achieves high accuracy on genotype clustering, doublet detection and ambient RNA estimation, as demonstrated across a range of challenging scenarios.