A critical question related to methods for typing CNVs is whether they usually arise from a single originating event and then are propagated with diminishing degrees of LD on a single haplotype background, or instead are frequently regenerated on varying haplotype backgrounds (18). The former situation would be conducive to tagging and indirect interrogation with HapMap-based genotyping platforms, while the latter would likely require direct interrogation or genomic sequencing for reliable association studies. Expansions and refinements of current genotyping platforms are increasingly focused on capturing CNVs adequately, and some success has already been achieved (19). Array and sequencing methods are also being used to type structural variants, using the HapMap samples for development and cross-validation of the methods (20, 21).
