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Conditional random pattern algorithm for LOH inference and segmentation

文献类型：期刊论文

作者Wu, Ling-Yun1,2; Zhou, Xiaobo1; Li, Fuhai1; Yang, Xiaorong1; Chang, Chung-Che3; Wong, Stephen T. C.1
刊名BIOINFORMATICS
出版日期2009
卷号25期号:1页码:61-67
ISSN号1367-4803
DOI10.1093/bioinformatics/btn561
英文摘要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).
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
语种英语
WOS记录号WOS:000261996400010
出版者OXFORD UNIV PRESS
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/8627]  
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.

入库方式： OAI收割

来源：数学与系统科学研究院

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