KMS Of Academy of mathematics and systems sciences, CAS
| RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data | |
Chen, Ziwei1,2; Gong, Fuzhou1,2 ; Wan, Lin1,2; Ma, Liang3
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| 2020-06-01 | |
| Source Publication | BIOINFORMATICS
 |
| ISSN | 1367-4803 |
| Volume | 36Issue:11Pages:3299-3306 |
| Abstract | 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 |
| Indexed By | SCI |
| Language | 英语 |
| Funding Project | 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 Research Area | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| WOS Subject | Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability |
| WOS ID | WOS:000550117300002 |
| Publisher | OXFORD UNIV PRESS |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/51808 |
| Collection | 应用数学研究所 |
| Corresponding Author | Wan, Lin; Ma, Liang |
| Affiliation | 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 |
| Recommended Citation 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. |
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