Table S2.
        Description of Methods Used for Imputation and Analysis in Each Cohort Included in the Genome-Wide Association (GWA) Meta-Analysis
Cohort,Genotyping Platform,Pre-Imputation Variant Filters,Pre-Imputation Sample Filters,Imputation Software,Post-Imputation Filters,Association Software
Call rate,MAF,HWE,Other filters,Call rate,Heterozygosity,Ethnicity,Sex mismatches,Other filters
ALSPAC,Illumina HumanHap550 quad-chip,0.95,0.01,5E-7,,0.97,Yes,Yes,Yes,>10% Identity by descent<comma> insufficient sample replication,Minimac and Mach,None,Mach2QTLV112
Generation R,Illumina Human 610 and 660 Quad Array,0.95,0.001,1E-7,,0.975,Yes,Yes,Yes,Relatedness,Minimac and Mach,None,Plink 1.07
GINI/LISA,Affymetrix 5.0 and Affymetrix 6.0,0.95,0.01,1E-5,,0.95,> 4 SD,,Yes,Similarity QC based on MDS,Impute v2.3.0,SNPTEST NA for BETA<comma> SE and P_VAL,SNPTEST v2.4.1
INMA,Illumina Human Omni1,0.95,0.01,1E-6,,0.98,,No,Yes,LRR SD > 0.3<comma> duplicates<comma> relatedness,Impute v.2,None,SNPtest v.2
MoBa,Illumina Human 660W Quad Array,0.97,0.01,1E-6,Mitochodrial SNPs<comma> chrY + PAR SNPs<comma> SNPs that could not be updated to hg37<comma> non-“rs” SNPs,0.96,> 4 SD,Yes,Yes,Relatedness,SHAPEIT (v2.r644)<comma> Impute (version 2.3.0),SNPTEST NA for BETA and P_VAL,SNPTEST v2.5-beta4
NTR,Affymetrix 6.0,0.95,0.01,1E-5,Double-typed error rate > 0.02<comma> Mendel error rate > 0.02<comma> allele frequency difference with reference set > 0.20<comma> C/G and A/T SNPs with MAF > 0.35,0.90,F > 0.10 or F < -0.10,No,Yes,IBS/IBD discrepencies<comma> Mendel error rate > 0.02,Minimac and Mach,Plink NA for BETA<comma> SE and P_VAL,Plink 1.07
Raine,Illumina Human 660W Quad Array,0.95,0.01,5.7E-7,C/G and A/T SNPs removed,0.97,F > 0.1875; heterozygosity > 0.30,No,Yes,,Mach,,
TEDS,Affymetrix 6.0,0.80,0.01,1E-20,SNPTEST info > 0.975,0.98,yes,Yes,Yes,Relatedness (IBD < 5%)<comma> regenotyping low concordance,Impute v2,None,Plink 1.07
TRAILS,Illumina Cyto SNP12 v2,0.95,0.01,1E-3,chr X SNPs >1% heterozygous in men,0.95,> 4 SD,Yes,Yes,Duplicates,Impute v2,Callrate 10%<comma> duplicates,SNPtest 2.4.1