Some studies have observed a differential taggability for common CNVs; these loci, it is argued, are less likely to be in strong LD (r2>0.8) with flanking markers than are frequency-matched SNPs. Several explanations have been proposed to account for this observed differential taggability, such as lower SNP density in regions near CNVs and the higher mutation rates of certain CNVs (producing greater allelic diversity nearby) than those of SNPs [2], [14], [15]. This observed difference in the magnitude of LD between CNVs and SNPs relative to LD among SNPs impacts, through its effect on allelic association, our ability to assess the phenotypic influence of CNVs. On the other side of this controversy, the recent genome-wide study of an extensive catalog of CNVs in 16,000 cases of eight common diseases has argued that CNVs are generally well-tagged by SNPs. Indeed, among 2- and 3- class CNVs that passed QC and had MAF>10%, the study found that nearly 80% were tagged by SNPs at r2>0.80. Consequently, replication of association results for CNVs can be conducted in an independent sample set by the
