A small number of SNPs had negative values for one or more beadscores. For some of these SNPs, the vast majority of beadscores had valid positive values with only a small number of slightly negative values. To allow such SNPs to be included in the analysis (hence maximizing genomic coverage), a small amount (+50) was added to negative beadscores. Each SNP was then assessed to see if >90% of SNPs had positive scores. If so, the small number (<10%) of negative scores were assumed to represent small positive values (+1). SNPs which still had one or more negative scores after this process were not analysed further. All SNPs designed to detect copy number variants (i.e., invariants) were discarded. SNPs were removed in the initial quality control based on their frequency in HapMap CEU reference samples (The International HapMap Consortium., 2003). 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
