Our tagSNP selection strategy uses Tagger, a well-documented tool for the selection and evaluation of tagSNPs from genotype data [44]. The main value of our tagSNP selection process is based on the fact that future targeted genotyping projects, as opposed to whole genome SNP scans, will combine variation information from public (HapMap) and private sources potentially derived from next-generation sequencing of individuals with phenotypes of interest. Our study design is capable of finding effects due to rare variants if subsequently tested in a large enough case/control resource. The strategy in which regional re-sequencing is done only after a region of interest is identified through a HapMap-based strategy, will generally not detect the effects of rare variants.
