before performing meta-analysis on the genome-wide association data, SNPs with poor imputation quality scores (rsq_hat < 0.3 in MACH, proper_info < 0.4 in IMPUTE or the ratio of observed to expected dosage variance < 0.3 in BIMBAM) and markers with a minor allele frequency < 1% were excluded for each study. All individual GWAS were genomic control corrected before meta-analysis.44 Individual study-specific genomic control values ranged from 0.98 to 1.08. (Supplementary Table 18D). A total of 2,483,766 autosomal SNPs were meta-analyzed across: 17, 16 and 13 studies for FN-BMD (Pooled, women-only, and men-only analyses, respectively) and 16, 13 and 12 studies for LS-BMD (Pooled, women-only, and men-only analyses, respectively). A total of 76,253 X-linked SNPs were meta-analyzed across: 14, 13 and 10 studies for LS and FN-BMD (Pooled, women-only, and men-only analyses, respectively). In our discovery analysis, we chose to implement a fixed effects models approach as it is generally preferable for the purposes of initial discovery, where the aim is to screen and identify as many of the true variants as possible.45,46 SNPs present in less than three studies
