In genotype data for the combined tagSNP set, generated in 493 healthy oldest old and 439 random individuals aged 40–50, only 7 out of 245 (2.4%) private re-sequencing tagSNPs were represented by 297 HapMap tagSNPs at r2 = 0.8. This shows that HapMap tagSNPs generally do not adequately represent, private re-sequencing SNPs. This analysis highlights a major challenge for genetic association studies. Using only HapMap SNPs, effects due to uncommon variants would often be missed.
