中国科学院机构知识库网格
Chinese Academy of Sciences Institutional Repositories Grid
首页 机构 成果 学者
  
  1. CAS IR Grid
  2. 数学与系统科学研究院
  3. 中国科学院数学与系统科学研究院
  4. 应用数学研究所
RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data

文献类型：期刊论文

作者Chen, Ziwei2,3; Gong, Fuzhou2,3; Wan, Lin2,3; Ma, Liang1
刊名BIOINFORMATICS
出版日期2020-06-01
卷号36期号:11页码:3299-3306
ISSN号1367-4803
DOI10.1093/bioinformatics/btaa172
英文摘要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.
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
语种英语
出版者OXFORD UNIV PRESS
WOS记录号WOS:000550117300002
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/51807]  
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, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China
2.Chinese Acad Sci, Acad Math & Syst Sci, NCMIS, Beijing 100190, Peoples R China
3.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, 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.

入库方式： OAI收割

来源：数学与系统科学研究院

浏览0
下载0
收藏0
其他版本

除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。