In the replication stage, we meta-analyzed results from: (1) individuals of European descent only (Rep-EUR); and (2) all replication cohorts with multiple ethnicities (Rep-All). Likewise we meta-analyzed results from discovery cohorts and European-descent-only replication cohorts (“Combined EUR”) from discovery cohorts and all replication cohorts (“Combined All”). To investigate and account for potential heterogeneities in allelic effects between studies, we also performed “trans-ethnic meta-analysis” using MANTRA
25 (link) in the replication sample that included all ethnic groups (“Rep-All”) and in the combined analysis of the discovery and all ethnic groups in the replication sample (“Combined All”).
A successful replication was considered if: (1) the association
p-value in the cumulative-meta-analysis (Combined EUR) was genome-wide significant (
p < 5 × 10
−8) and less than the discovery meta-analysis
p-value; or (2) the association
p-value in the meta-analysis of replication-cohorts only (Rep-EUR) was less than
p = 0.0024 (a Bonferroni-adjusted threshold at
p = 0.05/21 since there were a total of 21 tests performed for whole body and appendicular lean mass in Rep-EUR cohorts during replication). Using the METAL package we also estimated
I2 to quantify heterogeneity and
p-values to assess statistical significance for a total of eight associations that were replicated in the cumulative-meta-analysis (combined EUR, five SNPs for whole body and three for appendicular lean mass).
To estimate the phenotypic variance explained by the genotyped SNPs in the Framingham Heart Study (FHS), we used a restricted maximum likelihood model implemented in the GCTA (Genome-wide Complex Trait Analysis) tool package
57 (link), 58 (link) and adjusted for the same set of covariates included in our GWAS.
Finally, we examined associations between all imputed SNPs in/near five genes (
THRH,
GLYAT,
GREM1,
CNTF, and
PRDM16 including 60 kB up and downstream of the gene) and lean mass, as these genes have been implicated to have associations with lean mass in previous association studies
18 (link)–20 (link).
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