A CNV has been defined as a DNA segment that is 1 kb or larger and is present at variable copy numbers in comparison with a reference genome (40). Copy number variable regions (CNVRs) are regions covered by overlapping CNVs (41). The copy number characterization of 270 HapMap samples showed that ∼80% of observed copy number differences between pairs of individuals were due to common CNVs with an allele frequency of >5%, and >99% were derived from inheritance rather than from new duplication/deletion events (13). According to published recommendations (13,41), we defined common CNVRs as regions covering at least three consecutive CNV markers showing deletions or duplications in at least 5% of each set of GWAS cases, parents and controls. Thus, if several individual CNVs overlapped, we merged them in the same CNVR, so that most CNVRs represent a union of overlapping CNVs (19,42). For details on the resulting 244 CNVRs based on 8051 CNV markers with genomic positions based on genome build hg 18 (March 2006), see Table 1 and Figure 2.
