An Improved Algorithm for Tag SNP Selection Based on Pair-Wise Linkage Disequilibrium

The search for the association between complex diseases and single nucleotide polymorphisms (SNPs) or haplotypes has recently received great attention. For those studies, it is essential to use a small subset of informative SNPs, i.e., tag SNPs, accurately representing the rest of the SNPs. We devised an improved algorithm for tagSNP selection using the pair-wise r 2 criterion. We first break down large marker sets into separate partitions, where more exhaustive searches can replace the LDSelect algorithm for tagSNP selection. These exhaustive searches lead to smaller tagSNP sets being generated. Its performance was assessed using HapMap data.