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论文类型：期刊论文
发表时间：2009-07-01
发表刊物：JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS
收录刊物：SCIE、EI
卷号：229
期号：1
页面范围：168-174
ISSN号：0377-0427
关键字：Mutual information; Imputation method; Missing genotype data; Missing SNP site; Extension method
摘要：Mutual information can be used as a measure for the association of a genetic marker or a combination of markers with the phenotype. In this paper, we study the imputation of missing genotype data. We first utilize joint mutual information to compute the dependence between SNP sites, then construct a mathematical model in order to find the two SNP sites having maximal dependence with missing SNP sites, and further study the properties of this model. Finally, an extension method to haplotype-based imputation is proposed to impute the missing values in genotype data. To verify our method, extensive experiments have been performed, and numerical results show that our method is superior to haplotype-based imputation methods. At the same time, numerical results also prove joint mutual information can better measure the dependence between SNP sites. According to experimental results, we also conclude that the dependence between the adjacent SNP sites is not necessarily strongest. (C) 2008 Elsevier B.V. All rights reserved.