When the SNPs are considered individually, for all but one of the 1,271 lead SNPs, we fail to reject a null hypothesis of homogenous effects across cohorts at the Bonferroni-adjusted P value threshold of 0.05/1,271. We generated an omnibus test statistic for heterogeneity by summing the Cochran Q-statistics for heterogeneity across all 1,271 lead SNPs38. Because the software used for meta-analysis does not report Q-statistics, we inferred these values based on the reported heterogeneity P values. To do so, we treated each lead SNP as if it were available for each of the 71 cohorts in the meta-analysis, which implies that the Q-statistic for each lead SNP has a χ2 distribution with 70 degrees of freedom. The sum of these Q-statistics is therefore (approximately) χ2-distributed with 70 × 1,271 = 88,970 degrees of freedom. This gave us an omnibus Q-statistic of 91,830, with corresponding P value equal to 9.68 × 10−12.
