A novel statistical algorithm for enhancing the utility of HapMap data to design genomic association studies in non-HapMap populations.

The HapMap database should be effectively used in designing disease association studies in non-HapMap populations. The efficiency of portability of tagSNPs from HapMap to non-HapMap populations is widely variable. A new algorithm is proposed for selecting SNPs from HapMap for use in non-HapMap populations by simultaneously considering and combining data on allele frequencies and linkage-disequilibrium values in the four HapMap populations. Empirical comparison and validation of the algorithm are provided by using Tagger, available HapMap data and data from an Indian population. The proposed method is shown to be efficient and effective. A software implementing this algorithm is freely available.