Choosing a set of haplotype tagging SNPs from a larger set of diallelic loci

On typing a large number of SNPs within a small genomic region in European populations it is commonly found that there is rather little haplotype diversity — the observed haplotypes fall into rather few major groups with only minor differences between haplotypes within groups. Johnson et al. [1] suggested that linkage disequilibrium and haplotype diversity within the region can be captured by a much smaller subset of the markers, which they term “haplotype tagging SNPs” (htSNPs). This note describes one formal approach to the optimal choice of htSNPs.