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

作　　者：Guangsheng Pei Fangfang Yan Lukas M.Simon Yulin Dai Peilin Jia Zhongming Zhao 

机构地区：[1]Center for Precision Health,School of Biomedical Informatics,The University of Texas Health Science Center at Houston,Houston,TX 77030,USA [2]Therapeutic Innovation Center,Baylor College of Medicine,Houston,TX 77030,USA [3]Human Genetics Center,School of Public Health,The University of Texas Health Science Center at Houston,Houston,TX 77030,USA [4]MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences,Houston,TX 77030,USA [5]Department of Biomedical Informatics,Vanderbilt University Medical Center,Nashville,TN 37203,USA [6]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

出　　处：《Genomics, Proteomics & Bioinformatics》2023年第2期370-384,共15页基因组蛋白质组与生物信息学报(英文版)

基　　金：supported by National Institutes of Health grants(Grant Nos.R01LM012806R,I01DE030122,and R01DE029818);support from Cancer Prevention and Research Institute of Texas(Grant Nos.CPRIT RP180734 and RP210045),United States.

摘　　要：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 increasing 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 collection of human cell type expression profiles and marker genes.We used deCS to annotate scRNAseq data from various tissue types and systematically evaluated the annotation accuracy under different 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 computation 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 cellular mechanisms underlying disease pathogenesis.

关 键 词：Cell type-specific enrichment analysis scRNA-seq Cell type annotation Trait-cell type association Cell typemarkergene 

分 类 号：Q811.4[生物学—生物工程]