Evaluation of Beagle Genotype Imputation Method and an Application

Abstract

This study describes the genotype imputation method using the Beagle program and was completed with the aim of evaluating the imputation performance in three different scenarios. A population-based imputation method, the Beagle program uses linkage disequilibrium (LD) information between missing single nucleotid polimorfizm (SNP) and observed SNPs, the local haplotype cluster (Browning) model to offer high rates of imputation accuracy for estimation of deficient genotypes. With this aim, the study used 1356 SNP data from the 22nd chromosome of 191 individuals in the 1000 Genome project, cutting the dataset at random rates of 20%, 50% and 70% to create three different scenarios. The Allelic-R2 values obtained as a result of the three scenarios were larger than 90% and imputations with high degree of accuracy were made. In this study the differences in the size of the reference datasets in the Beagle program were not identified to have a clear effect on imputation accuracy. In conclusion, in terms of results obtained from samples with different sizes using the Beagle program, imputations with high accuracy could be made. © 2017, Centenary University. All rights reserved.