FastCAR: fast correction for ambient RNA to facilitate differential gene expression analysis in single-cell RNA-sequencing datasets.

Autor: Berg M; Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. m.berg@umcg.nl.; University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands. m.berg@umcg.nl., Petoukhov I; MIcompany, Amsterdam, The Netherlands., van den Ende I; MIcompany, Amsterdam, The Netherlands., Meyer KB; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Guryev V; University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands.; European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands., Vonk JM; University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands.; Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands., Carpaij O; University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands.; Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands., Banchero M; Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.; University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands., Hendriks RW; Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands., van den Berge M; University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands.; Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands., Nawijn MC; Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.; University of Groningen, University Medical Center Groningen, Groningen Research Institute, for Asthma and COPD (GRIAC), Groningen, The Netherlands.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2023 Nov 29; Vol. 24 (1), pp. 722. Date of Electronic Publication: 2023 Nov 29.
DOI: 10.1186/s12864-023-09822-3
Abstrakt: Cell type-specific differential gene expression analyses based on single-cell transcriptome datasets are sensitive to the presence of cell-free mRNA in the droplets containing single cells. This so-called ambient RNA contamination may differ between samples obtained from patients and healthy controls. Current ambient RNA correction methods were not developed specifically for single-cell differential gene expression (sc-DGE) analyses and might therefore not sufficiently correct for ambient RNA-derived signals. Here, we show that ambient RNA levels are highly sample-specific. We found that without ambient RNA correction, sc-DGE analyses erroneously identify transcripts originating from ambient RNA as cell type-specific disease-associated genes. We therefore developed a computationally lean and intuitive correction method, Fast Correction for Ambient RNA (FastCAR), optimized for sc-DGE analysis of scRNA-Seq datasets generated by droplet-based methods including the 10XGenomics Chromium platform. FastCAR uses the profile of transcripts observed in libraries that likely represent empty droplets to determine the level of ambient RNA in each individual sample, and then corrects for these ambient RNA gene expression values. FastCAR can be applied as part of the data pre-processing and QC in sc-DGE workflows comparing scRNA-Seq data in a health versus disease experimental design. We compared FastCAR with two methods previously developed to remove ambient RNA, SoupX and CellBender. All three methods identified additional genes in sc-DGE analyses that were not identified in the absence of ambient RNA correction. However, we show that FastCAR performs better at correcting gene expression values attributed to ambient RNA, resulting in a lower frequency of false-positive observations. Moreover, the use of FastCAR in a sc-DGE workflow increases the cell-type specificity of sc-DGE analyses across disease conditions.
(© 2023. The Author(s).)
Databáze: MEDLINE
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