Great care was taken in combining results from different samples and platforms to avoid confusing alleles, especially at palindromic SNPs. To check this, we inspected all SNPs whose range of allele frequencies in the meta-analysis was greater than 0.2, a commonly-used threshold. Most of these SNPs were palindromes and, as expected, their minimum and maximum allele frequencies across the study samples added to approximately 1. Using the “STRANDLABEL” and “USESTRAND ON” commands in METAL, these SNPs were recoded to ensure consistent allele coding across the samples analyzed. Because the German sample was genotyped on the Illumina platform that contains no palindromic SNPs, we used that sample as the gold standard. A final check identified 36 SNPs whose allele frequency ranges still exceeded 0.2. Most of these were not palindromes, and those that were did not show complementary allele frequencies. We concluded these were unreliable SNPs and dropped them from the analysis.
