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 drift >0.002 or WF>0.04 or <−0.04. For the US cohort we found an excess of CNVs in samples with LRR_SD values between 0.25 and 0.28, so the LRR_SD cut-off was reduced to 0.25 for both cases and controls from the US. All samples that failed QC after the wave adjustment procedure were removed. Due to the complications of hemizygosity in males and X-chromosome inactivation in females, all analyses were restricted to autosomes. Additionally, to ensure that we were working with high-confidence CNVs, we excluded any CNV for which the difference of the log likelihood of the most likely copy number state and the less likely copy number state was less than 10 (generated using the -conf function in PennCNV). Finally, some centromeric and telomeric regions are not well mapped, and this can potentially result in CNV-calling errors in these regions (Dr. Kai Wang, personal communication). Also, genomic regions coding for immunoglobulin genes have previously been shown to be potential sites
