The GIANT Consortium performed a meta-analysis of GWAS data in a discovery set with 133,653 and 123,865 individuals of recent European ancestry from 46 studies for height3 (link) and BMI4 (link), respectively. In each of the participating studies, genotype data were imputed to ~2.8 million SNPs present in the HapMap Phase 2 European-American reference panel26 (link), and the standard errors of all SNPs were adjusted by the genomic control method20 (link). We calculated the effective sample size for each SNP and excluded SNPs with effective sample sizes of >2 s.d. from the mean. We also excluded SNPs with MAF of <0.01, retaining ~2.5 million SNPs for both height and BMI.
We also obtained access to the individual-level genotype and phenotype data of the ARIC cohort, a population-based study of Americans28 (link), and the QIMR cohort, a twin study of Australians29 (link). The ARIC samples were genotyped by Affymetrix 6.0 SNP array, and the QIMR samples were genotyped by Illumina 610K or 370K array. After quality control filtering of SNPs, 593,521 and 274,604 genotyped SNPs were retained in the ARIC (excluding SNPs with missingness of >2%, MAF of <0.01 or Hardy-Weinberg equilibrium (HWE) P value of <1 × 10–3) and QIMR cohorts (excluding SNPs with missingness of >5%, MAF of <0.01 and HWE P value of <1 × 10–6), respectively. After sample quality control analysis, 8,682 and 11,742 individuals of European ancestry in the ARIC and QIMR cohorts, respectively, were included for further analysis. The quality control protocol has been detailed previously for the ARIC cohort18 (link),30 (link) and for the QIMR cohort14 (link),29 (link). We then estimated pairwise genetic relationships between individuals14 (link) and removed one of each pair of individuals with an estimated relatedness of >0.025. After these quality control steps, 6,654 and 3,924 unrelated individuals were retained in the ARIC and QIMR cohorts, respectively. All the ARIC samples were from adults and the QIMR samples were from 3,247 adults and 677 16-year-old adolescents. The SNP data for both ARIC and QIMR cohorts were imputed to the HapMap Phase 2 CEU panel by MACH31 (link). We used the best guess genotypes of the imputed SNPs and excluded imputed SNPs with HWE P value of <1 × 10–6, imputation R2 of <0.3 or MAF of <0.01 and retained 2,406,652 and 2,410,957 SNPs in the ARIC and QIMR cohorts, respectively. The ARIC cohort is part of the discovery sample of the GIANT meta-analysis, whereas the QIMR cohort is not. In the prediction analyses, the height and BMI phenotypes in the ARIC and QIMR cohorts were adjusted for age and sex effects and standardized to z scores14 (link),18 (link). In the QIMR cohort, only samples from 3,247 adults were used in the prediction analysis for BMI.
We also obtained access to the individual-level genotype and phenotype data of the ARIC cohort, a population-based study of Americans28 (link), and the QIMR cohort, a twin study of Australians29 (link). The ARIC samples were genotyped by Affymetrix 6.0 SNP array, and the QIMR samples were genotyped by Illumina 610K or 370K array. After quality control filtering of SNPs, 593,521 and 274,604 genotyped SNPs were retained in the ARIC (excluding SNPs with missingness of >2%, MAF of <0.01 or Hardy-Weinberg equilibrium (HWE) P value of <1 × 10–3) and QIMR cohorts (excluding SNPs with missingness of >5%, MAF of <0.01 and HWE P value of <1 × 10–6), respectively. After sample quality control analysis, 8,682 and 11,742 individuals of European ancestry in the ARIC and QIMR cohorts, respectively, were included for further analysis. The quality control protocol has been detailed previously for the ARIC cohort18 (link),30 (link) and for the QIMR cohort14 (link),29 (link). We then estimated pairwise genetic relationships between individuals14 (link) and removed one of each pair of individuals with an estimated relatedness of >0.025. After these quality control steps, 6,654 and 3,924 unrelated individuals were retained in the ARIC and QIMR cohorts, respectively. All the ARIC samples were from adults and the QIMR samples were from 3,247 adults and 677 16-year-old adolescents. The SNP data for both ARIC and QIMR cohorts were imputed to the HapMap Phase 2 CEU panel by MACH31 (link). We used the best guess genotypes of the imputed SNPs and excluded imputed SNPs with HWE P value of <1 × 10–6, imputation R2 of <0.3 or MAF of <0.01 and retained 2,406,652 and 2,410,957 SNPs in the ARIC and QIMR cohorts, respectively. The ARIC cohort is part of the discovery sample of the GIANT meta-analysis, whereas the QIMR cohort is not. In the prediction analyses, the height and BMI phenotypes in the ARIC and QIMR cohorts were adjusted for age and sex effects and standardized to z scores14 (link),18 (link). In the QIMR cohort, only samples from 3,247 adults were used in the prediction analysis for BMI.