Concerning the genome-wide agreement between CNVR calling in both discovery GWAS samples, a total of 880 CNVRs with frequencies >1% which cover ≈15% of the genome have been called in the family-based discovery GWAS sample. Of these CNVRs, 97.04% were again called as CNVRs in the case–control discovery GWAS sample. Even among those CNVRs that were found in at least two individuals (6473) in the family-based discovery GWAS sample, 83.5% were redetected as CNVRs in the case–control discovery GWAS sample. CNVRs called in just one individual are more likely false positives compared with CNVRs identified in several individuals and are thus neglected here.
