SNPs with CEU minor allele frequency <1% were dropped from further analysis (this reduced the number of 1M v1 SNPs of interest to ~800k SNPs and the number of 1M v3 SNPs of interest to ~920k SNPs). Removing SNPs which are likely to be monomorphic in our Caucasian samples is desirable as the subsequent normalization and analysis steps are designed primarily for SNPs which are polymorphic. Furthermore, SNPs with very low (or zero) minor allele frequencies are unlikely to show significant results in genetic association studies.
