HapMap provides linkage disequilibrium (LD) information on a sample of 3.7 
million SNPs that can be used for tag SNP selection in whole-genome association 
studies. HapMap can also be used for tag SNP selection in candidate genes, 
although its performance has yet to be evaluated against gene resequencing data, 
where there is near-complete SNP ascertainment. The Environmental Genome Project 
(EGP) is the largest gene resequencing effort to date with over 500 resequenced 
genes. We used HapMap data to select tag SNPs and calculated the proportions of 
common SNPs (MAF>or=0.05) tagged (rho2>or=0.8) for each of 127 EGP Panel 2 genes 
where individual ethnic information was available. Median gene-tagging 
proportions are 50, 80 and 74% for African, Asian, and European groups, 
respectively. These low gene-tagging proportions may be problematic for some 
candidate gene studies. In addition, although HapMap targeted nonsynonymous SNPs 
(nsSNPs), we estimate only approximately 30% of nonsynonymous SNPs in EGP are in 
high LD with any HapMap SNP. We show that gene-tagging proportions can be 
improved by adding a relatively small number of tag SNPs that were selected 
based on resequencing data. We also demonstrate that ethnic-mixed data can be 
used to improve HapMap gene-tagging proportions, but are not as efficient as 
ethnic-specific data. Finally, we generalized the greedy algorithm proposed by 
Carlson et al (2004) to select tag SNPs for multiple populations and implemented 
the algorithm into a freely available software package mPopTag.