We first tested the Aberdeen, Munich and US samples separately, and also separately compared a) deletions, b) duplications, and c) genomic regions affected by both types of CNV. The Munich cohort had 1,299 SNPs affected by deletions (with frequency ranging from 0.4% to 15%), 1,042 SNPs affected by duplications (0.04%–9.3%) and 202 SNPs affected by both deletions and duplications (in different subjects; frequency 0.5%–9.4%). The equivalent values for Aberdeen were 3,879 deletions (0.34%–18.9%), 2,634 duplications (0.34%–17.5%) and 1,016 SNPs affected by both (0.45%–62%) and for the US cohort, 2,702 deletions (0.72%–46.7%), 3,159 duplications (0.72%–21%) and 1,399 SNPs affected by both (1.0%–58%). It should be noted that these CNVs have not been individually validated either by inspection in BeadStudio or by any experimental means, and many of these are likely to be false positives. The three cohorts differed both in the CNVs that most strongly associated and in the direction of the effects. There were no events that were significantly associated (p<0.05) in more than one cohort.
