Effect of Genotype Errors on the LD Measure for QTL Mapping

Objective To investigate the influence of genotyping error on linkage disequilibrium (LD) measure lx for mapping quantitative trait locus (QTL). Methods The properties of the LD measure for QTL mapping are investigated, in the absence and presence of genotyping errors, by using an analytic and simulation study. Results The lx values become smaller,with increase in genotyping errors,in a dose-dependent manner. Conclusion The decrease in lx values exceeds 50% as genotyping errors rate reaches 0. 03, especially when the marker allele frequencies are relatively high. The effects of the genotype errors are also confirmed via a simulation study using the haplotype frequencies of 10 different SNPs of ACE genes. Key words: Linkage disequilibrium;  Genotyping errors;  Quantitative trait locus;  Fine mapping