RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data

doi:10.1093/bioinformatics/btaa172

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	RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data
	Chen, Ziwei 1,2; Gong, Fuzhou1,2 ; Wan, Lin 1,2; Ma, Liang 3
	2020-06-01
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	36 期号:11 页码:3299-3306
摘要	Motivation: Single-cell sequencing (SCS) data provide unprecedented insights into intratumoral heterogeneity. With SCS, we can better characterize clonal genotypes and reconstruct phylogenetic relationships of tumor cells/ clones. However, SCS data are often error-prone, making their computational analysis challenging. Results: To infer the clonal evolution in tumor from the error-prone SCS data, we developed an efficient computational framework, termed RobustClone. It recovers the true genotypes of subclones based on the extended robust principal component analysis, a low-rank matrix decomposition method, and reconstructs the subclonal evolutionary tree. RobustClone is a model-free method, which can be applied to both single-cell single nucleotide variation (scSNV) and single-cell copy-number variation (scCNV) data. It is efficient and scalable to large-scale datasets. We conducted a set of systematic evaluations on simulated datasets and demonstrated that RobustClone outperforms state-of-the-art methods in large-scale data both in accuracy and efficiency. We further validated RobustClone on two scSNV and two scCNV datasets and demonstrated that RobustClone could recover genotype matrix and infer the subclonal evolution tree accurately under various scenarios. In particular, RobustClone revealed the spatial progression patterns of subclonal evolution on the large-scale 10X Genomics scCNV breast cancer dataset.
DOI	10.1093/bioinformatics/btaa172
收录类别	SCI
语种	英语
资助项目	National Key R&D Program of China[2018YFB0704304] ; National Natural Science Foundation of China[11571349] ; National Natural Science Foundation of China[91630314] ; National Natural Science Foundation of China[81673833] ; National Natural Science Foundation of China[11971459] ; Strategic Priority Research Program of CAS[XDB13050000] ; National Center for Mathematics and Interdisciplinary Sciences of CAS ; LSC of CAS ; Youth Innovation Promotion Association of CAS
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000550117300002
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/51808
专题	应用数学研究所
通讯作者	Wan, Lin; Ma, Liang
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, NCMIS, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China 3.Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China
推荐引用方式 GB/T 7714	Chen, Ziwei,Gong, Fuzhou,Wan, Lin,et al. RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data[J]. BIOINFORMATICS,2020,36(11):3299-3306.
APA	Chen, Ziwei,Gong, Fuzhou,Wan, Lin,&Ma, Liang.(2020).RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data.BIOINFORMATICS,36(11),3299-3306.
MLA	Chen, Ziwei,et al."RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data".BIOINFORMATICS 36.11(2020):3299-3306.