New methods for imputation of missing genotype using linkage disequilibrium and haplotype information

In this paper, we propose new missing imputation methods for the missing genotype data of single nucleotide polymorphism (SNP). The common objective of imputation methods is to minimize the loss of information caused by experimental missing elements. In general, imputation of missing genotype data has used a major allele method, but this approach is not far from the objective of the imputation - minimizing the loss of information. This method generally produces high error rates of missing value estimation, since the characteristics of the genotype data are not considered over the structure of given genotype data. In our methods, we use the linkage disequilibrium and haplotype information for the missing SNP genotype. As a result, we provide the results of the comparative evaluation of our methods and major allele imputation method according to the various randomized missing rates. (C) 2006 Elsevier Inc. All rights reserved.