A fast haplotype inference method for large population genotype data

doi:10.1016/j.csda.2008.04.004

CSpace > 应用数学研究所

	A fast haplotype inference method for large population genotype data
	Zhang, Ji-Hong 2,3; Wu, Ling-Yun1 ; Chen, Jian 2; Zhang, Xiang-Sun1
	2008-07-15
发表期刊	COMPUTATIONAL STATISTICS & DATA ANALYSIS
ISSN	0167-9473
卷号	52 期号:11 页码:4891-4902
摘要	With the rapid progress of genotyping techniques, many large-scale, genome-wide disease studies are now under way. One of the challenges of large disease-association studies is developing a fast and accurate computing method for haplotype inference from genotype data. In this paper, a new computing method for Population-based haplotype inference problem is proposed. The designed method does not assume haplotype blocks in the population and allows each individual haplotype to have its own structure, and thus is able to accommodate recombination and obtain higher adaptivity to the genotype data, specifically in the case of long marker maps. This method develops a dynamic programming algorithm, which is theoretically guaranteed to find exact maximum likelihood solutions of the variable order Markov chain model for haplotype inference problem within linear running time. Hence, it is fast and, as a result, practicable for large genotype datasets. Through extensive computational experiments on large-scale real genotype data, the proposed method is shown to be fast and efficient. (C) 2008 Elsevier B.V. All rights reserved.
DOI	10.1016/j.csda.2008.04.004
语种	英语
WOS研究方向	Computer Science ; Mathematics
WOS类目	Computer Science, Interdisciplinary Applications ; Statistics & Probability
WOS记录号	WOS:000258259600002
出版者	ELSEVIER SCIENCE BV
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/6902
专题	应用数学研究所
通讯作者	Wu, Ling-Yun
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Ctr Bioinformat, Beijing 100190, Peoples R China 2.Tsinghua Univ, Sch Econ & Management, Beijing 100084, Peoples R China 3.Beijing Foreign Studies Univ, Sch Int Business, Beijing 100089, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Ji-Hong,Wu, Ling-Yun,Chen, Jian,et al. A fast haplotype inference method for large population genotype data[J]. COMPUTATIONAL STATISTICS & DATA ANALYSIS,2008,52(11):4891-4902.
APA	Zhang, Ji-Hong,Wu, Ling-Yun,Chen, Jian,&Zhang, Xiang-Sun.(2008).A fast haplotype inference method for large population genotype data.COMPUTATIONAL STATISTICS & DATA ANALYSIS,52(11),4891-4902.
MLA	Zhang, Ji-Hong,et al."A fast haplotype inference method for large population genotype data".COMPUTATIONAL STATISTICS & DATA ANALYSIS 52.11(2008):4891-4902.