The recent release [7] of a reference map of human CNVs in the HapMap populations promises to shed light on the role of these variants in disease pathogenesis. On the other hand, a recent comprehensive study [8] involving 16,000 cases of eight common diseases and 3000 shared controls strongly suggests that CNVs are likely to make a relatively minor contribution to disease susceptibility. In the present study, we approached the investigation of this important topic by exploring evidence of enrichment of CNVs among trait-associated loci in disease susceptibility and in disease classes, as represented by the NHGRI catalog of reproducible associations from genome-wide association scans [9], for certain classes of CNVs, and by conducting a comprehensive functional characterization of CNVs as expression quantitative trait loci (eQTLs). The former seeks to evaluate the genetic information contained in CNVs in regard to disease risk and other complex traits; the latter assesses the functional impact of CNVs on the transcriptome, through which they may contribute to or cause disease phenotypes and other complex traits [10].
