首页|deCS:A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues

deCS:A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues

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Single-cell RNA sequencing(scRNA-seq)is revolutionizing the study of complex and dynamic cellular mechanisms.However,cell type annotation remains a main challenge as it largely relies on a priori knowledge and manual curation,which is cumbersome and subjective.The increas-ing number of scRNA-seq datasets,as well as numerous published genetic studies,has motivated us to build a comprehensive human cell type reference atlas.Here,we present decoding Cell type Specificity(deCS),an automatic cell type annotation method augmented by a comprehensive collec-tion of human cell type expression profiles and marker genes.We used deCS to annotate scRNA-seq data from various tissue types and systematically evaluated the annotation accuracy under dif-ferent conditions,including reference panels,sequencing depth,and feature selection strategies.Our results demonstrate that expanding the references is critical for improving annotation accuracy.Compared to many existing state-of-the-art annotation tools,deCS significantly reduced computa-tion time and increased accuracy.deCS can be integrated into the standard scRNA-seq analytical pipeline to enhance cell type annotation.Finally,we demonstrated the broad utility of deCS to identify trait-cell type associations in 51 human complex traits,providing deep insights into the cel-lular mechanisms underlying disease pathogenesis.All documents for deCS,including source code,user manual,demo data,and tutorials,are freely available at https://github.com/bsm1320/deCS.

Cell type-specific enrichment analysisscRNA-seqCell type annotationTrait-cell type associationCell type marker gene

Guangsheng Pei、Fangfang Yan、Lukas M.Simon、Yulin Dai、Peilin Jia、Zhongming Zhao

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Center for Precision Health,School of Biomedical Informatics,The University of Texas Health Science Center at Houston,Houston,TX 77030,USA

Therapeutic Innovation Center,Baylor College of Medicine,Houston,TX 77030,USA

CAS Key Laboratory of Genomic and Precision Medicine,Beijing Institute of Genomics,Chinese Academy of Sciences and China National Center for Bioinformation,Beijing 100101,China

Human Genetics Center,School of Public Health,The University of Texas Health Science Center at Houston,Houston,TX 77030,USA

MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences,Houston,TX 77030,USA

Department of Biomedical Informatics,Vanderbilt University Medical Center,Nashville,TN 37203,USA

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National Institutes of Health grantsNational Institutes of Health grantsNational Institutes of Health grantsCancer Prevention and Research Institute of Texas,United StatesCancer Prevention and Research Institute of Texas,United States

R01LM012806R01DE030122R01DE029818CPRIT RP180734RP210045

2023

10.1016/j.gpb.2022.04.001

基因组蛋白质组与生物信息学报(英文版)
中国科学院北京基因组研究所

基因组蛋白质组与生物信息学报(英文版)

CSTPCDCSCD
影响因子：0.495
ISSN：1672-0229
年,卷(期)：2023.21(2)
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