Current-generation high-throughput geno-typing platforms are extraordinarily efficient at genotyping SNPs but are less effective at geno-typing structural variants, such as insertions, deletions, inversions, and copy number variants (CNVs). These variants are common in the human genome, though not as common as SNPs (15). The HapMap was not designed to capture these variants, although it can be used indirectly to do so, particularly for deletions that are in strong LD with SNPs (16). CNVs, in which stretches of genomic sequence roughly 1 kb to 3 Mb in size are deleted or dupli-cated in varying numbers, have gained increasing attention because of their apparent ubiquity and potential dosage effect on gene expression (17).
