To examine whether CNVs represent genetic risk factors for obesity, we analyzed CNV calls on 430 obese case and 379 control subjects who were genotyped by Illumina SNP arrays and passed quality-control measures for CNV analysis. The sample characteristics were described in Table 1. We first compared the general characteristics of CNV calls between case and control subjects. The number of CNVs per subject did not differ between case and control subjects (5.8 ± 3.3 vs. 6.0 ± 3.1, P = 0.35). The number of gene-disrupting CNVs per subject is similar in case versus control subjects (3.8 ± 3.1 vs. 4.2 ± 2.7, P = 0.07). Similarly, the number of exonic CNVs per subject is similar in case versus control subjects (3.2 ± 2.9 vs. 3.6 ± 2.6, P = 0.06). We compiled a list of common CNV regions and found that 38.2% of CNV calls can be classified as rare CNVs. The number of rare CNVs per subject did not differ between obese case and control subjects (2.3 ± 2.4 vs. 2.2 ± 1.8, P = 0.41).
