To test for effects of common CNVs that may not be well captured by PennCNV calling algorithms from Infinium HumanHap SNP data, we next examined a set of SNPs shown to tag copy number polymorphisms (CNPs), as defined in McCarroll et al. [42] and provided by Drs. McCarroll and Altshuler (personal communication). Of 285 total HapMap tagging SNPs, we found that 169 and 202 of them were either directly represented or had a proxy of r2≥0.8 on the HumanHap310 and Human610-quad BeadChips, respectively. We then specifically examined the association statistics for these CNP-tagging SNPs in Aberdeen and Munich (combined) and in the US cohort. None of the association p values stood up to correction for the total SNPs tested, neither did any CNP-tagging SNP associate at p<0.05 (uncorrected) in both populations. We can therefore provide no evidence for the role of common CNVs in schizophrenia. However, it should be noted that many common CNVs cannot be detected using the HumanHap300 and 550 genotyping platforms [42], so it is not possible for us to conclusively rule out effects of common CNVs on schizophrenia.
