CNVs identified by 3 independent programs were validated in subjects carrying the variant with quantitative PCR (qPCR). We selected a TaqMan CNV probe in the target region. The probe was predesigned by Applied Biosystems (Applied Biosytems, Foster City, CA, USA). Genomic DNA was analyzed with real-time PCR using an ABI-7900 Fast PCR system. Each real-time PCR run included within-plate duplicates. Correction for sample-to-sample variation was done by simultaneously amplifying a standard CNV reference assay, RNAse P. Real-time data were analyzed using the comparative Ct method (Muller et al., 2002). The Ct values of each sample were normalized with the Ct value for the RNAse P assay. Only the samples with a standard error <0.15 were analyzed. Copy numbers were calculated using ABI CopyCaller™ Software v1.0.
