To examine the credibility of the MTAG-identified lead SNPs of our lowest-powered GWAS, Cognitive Performance, we conducted a replication analysis. We re-ran MTAG with GWAS results that exclude COGENT cohorts, and we used the COGENT meta-analysis as our replication sample. In addition to applying the MTAG filters above, we limited the analysis to SNPs for which the COGENT results file contains summary statistics based on analyses of at least 25,000 individuals. The MTAG-identified lead SNPs for Cognitive Performance from our restricted sampled are reported in Supplementary Table 44. We used our Bayesian framework to calculate the expected replication record of the MTAG results under the hypothesis that the MTAG-identified lead SNPs are true positives, given sampling variation and adjusted for winner’s curse and differences in SNP heritability across the samples.
