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Indexed by:期刊论文

Date of Publication:2009-07-01

Journal:JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS

Included Journals:SCIE、EI

Volume:229

Issue:1

Page Number:168-174

ISSN No.:0377-0427

Key Words:Mutual information; Imputation method; Missing genotype data; Missing SNP site; Extension method

Abstract: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.