Conditional random pattern algorithm for LOH inference and segmentation

doi:10.1093/bioinformatics/btn561

CSpace > 应用数学研究所

	Conditional random pattern algorithm for LOH inference and segmentation
	Wu, Ling-Yun1,2 ; Zhou, Xiaobo 1; Li, Fuhai 1; Yang, Xiaorong 1; Chang, Chung-Che 3; Wong, Stephen T. C.1
	2009
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	25 期号:1 页码:61-67
摘要	Motivation: Loss of heterozygosity (LOH) is one of the most important mechanisms in the tumor evolution. LOH can be detected from the genotypes of the tumor samples with or without paired normal samples. In paired sample cases, LOH detection for informative single nucleotide polymorphisms (SNPs) is straightforward if there is no genotyping error. But genotyping errors are always unavoidable, and there are about 70% non-informative SNPs whose LOH status can only be inferred from the neighboring informative SNPs. Results: This article presents a novel LOH inference and segmentation algorithm based on the conditional random pattern (CRP) model. The new model explicitly considers the distance between two neighboring SNPs, as well as the genotyping error rate and the heterozygous rate. This new method is tested on the simulated and real data of the Affymetrix Human Mapping 500K SNP arrays. The experimental results show that the CRP method outperforms the conventional methods based on the hidden Markov model (HMM).
DOI	10.1093/bioinformatics/btn561
语种	英语
资助项目	TMHRI scholarship award ; National Science Foundation of China[60503004] ; 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:000261996400010
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/8628
专题	应用数学研究所
通讯作者	Zhou, Xiaobo
作者单位	1.Cornell Univ, Dept Radiol, Ctr Biotechnol & Informat, Methodist Hosp,Res Inst,Weill Med Coll, Houston, TX 77030 USA 2.Chinese Acad Sci, Inst Appl Math, Acad Math & Syst Sci, Beijing 100080, Peoples R China 3.Cornell Univ, Dept Pathol, Methodist Hosp, Weill Med Coll, Houston, TX 77030 USA
推荐引用方式 GB/T 7714	Wu, Ling-Yun,Zhou, Xiaobo,Li, Fuhai,et al. Conditional random pattern algorithm for LOH inference and segmentation[J]. BIOINFORMATICS,2009,25(1):61-67.
APA	Wu, Ling-Yun,Zhou, Xiaobo,Li, Fuhai,Yang, Xiaorong,Chang, Chung-Che,&Wong, Stephen T. C..(2009).Conditional random pattern algorithm for LOH inference and segmentation.BIOINFORMATICS,25(1),61-67.
MLA	Wu, Ling-Yun,et al."Conditional random pattern algorithm for LOH inference and segmentation".BIOINFORMATICS 25.1(2009):61-67.