Depending on the size of the candidate region, and the cost implications, the investigator can choose to include all potentially functional SNPs (localised in predicted regulatory regions, splice sites, intergenic sequence, introns or coding exons) in marker selection, supplemented by a selection of tagSNPs, or rely on the use of tagSNPs alone to cover the gene/region. Selecting markers on the basis of functional annotation alone is not recommended, since the causative polymorphism may not have been identified yet, or may be in a region that has to date been deemed ‘non-functional’ 12. Of course, if a specific study is aimed at replicating and/or fine mapping a candidate region suggested by the results of a previous study, it is imperative that the SNP associated in the original study is included in the design.
