MEGA SAMPLES VOL-103

In addition, we tested the two loci for association in each of the three available HapMap Phase II samples (CHB, YRI and CEU). We also tested the loci in 14 additional samples of self-reported European descent for association with all eight traits. These samples were genotyped on either the MEGA or the Affymetrix arrays. These samples include the GALA study from Finland and the EPIC-Norfolk study from the UK. We also tested the loci in 49 samples from the four extreme phenotypes (lowest and highest quintiles for each trait) using the same method as in the discovery stage. These samples were genotyped on the Illumina arrays.

The two novel loci were tested using SPU and METAL for univariate associations. Because of the linkage disequilibrium (LD) structure of the HapMap Phase II CEU samples, haplotypes were inferred from the genotyped variants in the UK Biobank samples and tested in these samples. In the discovery stage, we tested the association of each genetic variant with the rank-based inverse-normally transformed residual values in MEGA samples and in each individual study, respectively. These association analyses were performed using SUGEN, which is based on generalized estimating equations (GEE) allowing correlated errors for first or second-degree relatives and independent error distributions by self-reported race/ethnic group [41]. Association results from these studies were then combined through fixed-effect inverse-variance-weighted meta-analysis in METAL for each trait [42]. Both ancestry-combined and ancestry-specific meta-analyses were performed. Complete summary level results are available through dbGaP (phs000356).

In the replication stage, we tested the association of each genetic variant with the rank-based inverse-normally transformed residual values in the independent samples of BCX. This sample does not include any of the HapMap Phase II samples as no additional genotypes were available (Supplemental Table 5). Association analyses were performed using the additive linear regression model, adjusting for age, age2, sex (when applicable), center (when applicable), and the first 10 PCs calculated from an LD-pruned set of genotypes in each individual study. These association results were combined using inverse-variance-weighted meta-analysis in METAL for each trait [42].

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