For quality control of genotyped GWAS results, we removed SNPs with MAF of < 0.1%, a Hardy-Weinberg P <10−20 in Europeans, or a call rate of < 90%. We also removed SNPs that were only genotyped on the 23andMe V1 platform, due to limited sample size, and SNPs on chrM or chrY. Using trio data, we removed SNPs that failed a test for parent-offspring transmission; specifically, we regressed the child’s allele count against the mean parental allele count and removed SNPs with fitted β < 0.6 and P < 10−20 for a test of β < 1. We also tested genotyped SNPs for genotype date effects, and removed SNPs with P < 10−50 by ANOVA of SNP genotypes against a factor dividing genotyping date into 20 roughly equal-sized buckets. For imputed GWAS results, we removed SNPs with average r2 < 0.50 or minimum r2 < 0.30 in any imputation batch, as well as SNPs that had strong evidence of an imputation batch effect. The batch effect test is an F test from an ANOVA of the SNP dosages against a
