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题名A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns
作者
发表日期2017-12-01
发表期刊Scientific Reports
卷号7期号:1
摘要

Variations in DNA copy number carry important information on genome evolution and regulation of DNA replication in cancer cells. The rapid development of single-cell sequencing technology enables exploration of gene-expression heterogeneity among single cells, providing important information on cell evolution. Evolutionary relationships in accumulated sequence data can be visualized by adjacent positioning of similar cells so that similar copy-number profiles are shown by block patterns. However, single-cell DNA sequencing data usually have low amount of starting genome, which requires an extra step of amplification to accumulate sufficient samples, introducing noise and making regular pattern-finding challenging. In this paper, we will propose to tackle this issue of recovering the hidden blocks within single-cell DNA-sequencing data through continuous sample permutations such that similar samples are positioned adjacently. The permutation is guided by the total variational norm of the recovered copy number profiles, and is continued until the total variational norm is minimized when similar samples are stacked together to reveal block patterns. An efficient numerical scheme for finding this permutation is designed, tailored from the alternating direction method of multipliers. Application of this method to both simulated and real data demonstrates its ability to recover the hidden structures of single-cell DNA sequences.

DOI10.1038/s41598-017-09139-8
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收录类别SCIE
语种英语English
WOS研究方向Science & Technology - Other Topics
WOS类目Multidisciplinary Sciences
WOS记录号WOS:000408535700011
Scopus入藏号2-s2.0-85028473008
引用统计
被引频次:2[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符https://repository.uic.edu.cn/handle/39GCC9TT/6345
专题理工科技学院
通讯作者Cheung, Yiu-ming
作者单位
1.Electrical and Information College of Jinan,University,Zhuhai,China
2.Department of Computer Science,Hong Kong Baptist University China,Hong Kong,China
3.HKBU Institute of Research and Continuing Education,Shenzhen,China
4.BNU-HKBU United International College,Zhuhai,China
通讯作者单位北师香港浸会大学
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Zhang, Yue,Cheung, Yiu-ming,Su, Weifeng. A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns[J]. Scientific Reports, 2017, 7(1).
APA Zhang, Yue, Cheung, Yiu-ming, & Su, Weifeng. (2017). A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns. Scientific Reports, 7(1).
MLA Zhang, Yue,et al."A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns". Scientific Reports 7.1(2017).
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