An Application to Select Tag Loci by Using Hierarchical Structures of DNA Markers

A domain where recombination does not occur often, yet maintained linkage disequilibrium exists on DNA sequence is known as a ‘haplotype block’ or ‘Linkage Disequilibrium (LD) block’. Many methods are available to identify haplotype blocks using disequilibrium parameters, such as the well-known Gabriel’s method on Haploview, and so on. After identifying hyplotype blocks, we can also select tagging SNPs (single nucleotide polymorphisms) for these hyplotype blocks such as Tagger on Haploview, etc. We considered that Echelon analysis can be applied to identify hyplotype block and to select tagging SNPs, and report herein that the comprehensive method can be applied according to our new method using Echelon analysis. Finally we evaluated about the comparison of results between our method and others, using real data.