All subjects that passed SNP QC procedures were entered into the CNV analysis. This comprised 892 samples from Aberdeen (441 controls, 451 cases), 842 samples from Munich (412 controls, 430 cases) and 443 samples from the US (267 controls, 176 cases). The CNV calls were generated using the PennCNV software (version 2008jun26 version [62]) using the Log R ratio (LRR) and B allele frequency (BAF) measures automatically computed from the signal intensity files by BeadStudio, and the standard hg18 “all” PennCNV hidden Markov model (hmm) and population frequency of B allele (pfb) files for the 317 and 550 BeadChips. For the samples genotyped on the 610-Quad BeadChips, we used the hh550_610.hg18 pfb and gc model files separately provided by Dr. Kai Wang to ensure inclusion of all CNV-specific markers. Because many of the samples had below optimal genomic wave QC values, for Aberdeen and Munich we implemented the gc model wave adjustment procedure. We used the PennCNV checks to exclude samples that failed quality control. These included samples that had a LRR standard deviation >0.28, BAF median>0.55 or <0.45, BAF
