Efficient simulation under a population genetics model of carcinogenesis

doi:10.1093/bioinformatics/btr025

CSpace > 应用数学研究所

	Efficient simulation under a population genetics model of carcinogenesis
	Zhu, Tianqi 2; Hu, Yucheng 2; Ma, Zhi-Ming3 ; Zhang, De-Xing 1; Li, Tiejun 2; Yang, Ziheng 1,4,5
	2011-03-15
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	27 期号:6 页码:837-843
摘要	Motivation: Cancer is well known to be the end result of somatic mutations that disrupt normal cell division. The number of such mutations that have to be accumulated in a cell before cancer develops depends on the type of cancer. The waiting time T(m) until the appearance of m mutations in a cell is thus an important quantity in population genetics models of carcinogenesis. Such models are often difficult to analyze theoretically because of the complex interactions of mutation, drift and selection. They are also computationally expensive to simulate because of the large number of cells and the low mutation rate. Results: We develop an efficient algorithm for simulating the waiting time T(m) until m mutations under a population genetics model of cancer development. We use an exact algorithm to simulate evolution of small cell populations and coarse-grained tau-leaping approximation to handle large populations. We compared our hybrid simulation algorithm with the exact algorithm in small populations and with available asymptotic results for large populations. The comparison suggested that our algorithm is accurate and computationally efficient. We used the algorithm to study the waiting time for up to 20 mutations under a Moran model with variable population sizes. Our new algorithm may be useful for studying realistic models of carcinogenesis, which incorporates variable mutation rates and fitness effects. Contact: z.yang@ucl.ac.uk
DOI	10.1093/bioinformatics/btr025
语种	英语
资助项目	National Science Foundation of China[10871010] ; National Basic Research Program[2005CB321704] ; MOST[2006CB805901] ; K.C. Wong Education Foundation, Hong Kong
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:000288277300014
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/12688
专题	应用数学研究所
通讯作者	Yang, Ziheng
作者单位	1.Chinese Acad Sci, Inst Zool, Beijing 100101, Peoples R China 2.Peking Univ, Sch Mat Sci, Beijing 100871, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 4.Peking Univ, Coll Life Sci, Beijing 100871, Peoples R China 5.UCL, Dept Biol, London WC1E 6BT, England
推荐引用方式 GB/T 7714	Zhu, Tianqi,Hu, Yucheng,Ma, Zhi-Ming,et al. Efficient simulation under a population genetics model of carcinogenesis[J]. BIOINFORMATICS,2011,27(6):837-843.
APA	Zhu, Tianqi,Hu, Yucheng,Ma, Zhi-Ming,Zhang, De-Xing,Li, Tiejun,&Yang, Ziheng.(2011).Efficient simulation under a population genetics model of carcinogenesis.BIOINFORMATICS,27(6),837-843.
MLA	Zhu, Tianqi,et al."Efficient simulation under a population genetics model of carcinogenesis".BIOINFORMATICS 27.6(2011):837-843.