The most promising new region detected in the two GWAS samples, a CNVR at chromosome 11q11 (CNVR 11q11), was technically validated in the family-based GWAS sample using qPCR to ensure reliability of the chip-based CNVR detection and for additional analyses based on precise individual copy number calls. In more detail, we applied real-time quantitative PCR, using a Duplex TaqMan CNV assay (Applied Biosystems, Germany; assay Hs03802074_cn at chr11:55 203 791 ± 50 bp) as described previously (43). Briefly, every reaction was performed as a triplicate and the results for the qPCR were analysed using the software CopyCaller 1.0 (Applied Biosystems). Overall, the correlation between continuous intensity-based CNV calls used for association testing and continuous qPCR predicted calls was estimated to be 0.87 (Pearson correlation coefficient). Using qPCR approximately half of the individuals of the family-based sample were identified as carriers of a heterozygous or homozygous deletion at CNVR 11q11. Regarding called CNS the data were not readily comparable. Hence, all called 105 homozygous deletions at CNVR 11q11 were called by both qPCR and Affymetrix CNV markers whereas the overlap for
