Supplementary Table 2 shows the SNP quality control criteria used in the eligible 88 GWA reports. In 69 of those, the individual studies had used non-identical quality control criteria and in only 18 there was apparent uniformity among the individual studies (report did not provide details but referred to previous publications). Minor allele frequency (MAF), SNP call rate and deviation from Hardy-Weinberg equilibrium (HWE) were among the most common parameters applied. A MAF cut-off of 1% was used for inclusion of SNPs in the analyses in 41 reports, while 4 reports included SNP with MAF of 5% or more, 3 included SNPs with MAF of 2% or more and 1 report included SNPs with MAF of 0.1% or more. When information was provided, 11 reports used a SNP call rate cut-off of 95%, 4 used a cut-off of 90%, 1 used 97%, 4 used 98%, and 2 used 99%. The P-value used to denote deviation from HWE varied from 10−4 to 10−7, with only 1 study using P=5×10−20. Twenty-one reports used some additional stated criterion other than MAF, HWE and
