小柯机器人

英国威康桑格研究所Mara K. N. Lawniczak、Martin Hemberg、Haynes Heaton等研究人员合作开发了单细胞RNA测序数据聚类分析的新技术。该项研究成果于2020年5月4日在线发表在《自然—方法学》杂志上。

Title: Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

Author: Haynes Heaton, Arthur M. Talman, Andrew Knights, Maria Imaz, Daniel J. Gaffney, Richard Durbin, Martin Hemberg, Mara K. N. Lawniczak

Issue&Volume: 2020-05-04

Abstract: 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.

DOI: 10.1038/s41592-020-0820-1

Source: https://www.nature.com/articles/s41592-020-0820-1

Nature Methods：《自然—方法学》，创刊于2004年。隶属于施普林格·自然出版集团，最新IF：47.99
官方网址：https://www.nature.com/nmeth/
投稿链接：https://mts-nmeth.nature.com/cgi-bin/main.plex