Haplotype tag selection
Selecting haplotype-tag SNPs (ht-SNPs) can systematically and efficiently refine the process of haplotype construction and reduce the marker number for genotyping. In this study, three htSNPs (5'flankingSNP1, in2SNP1, in6SNP1) were selected to represent all haplotypes with frequencies larger than 2% using SNPtagger software [41] (Table 5). Results from the htSNP analysis suggest that the information obtained by examining three SNPs (instead of 10) should be sufficient for genetic analysis, since these can be used to construct and represent all common haplotypes with frequency >2%. Five haplotypes were constructed using these 3 htSNPs and statistical analyses detected no differences in haplotype distributions between cases and controls (Table 5).