Samples were genotyped on the Metabochip at the Human Genetics Center of the University of Texas-Houston (ARIC, GenNet and HyperGEN), the University of Southern California Epigenome Center (MEC), and the Translational Genomics Research Institute (WHI). Each center also genotyped 90 HapMap YRI (Yoruba in Ibadan, Nigeria) samples to facilitate cross-study quality control (QC), as well as 2–3% study-specific blinded replicates to assess genotyping reproducibility. Genotypes were called separately for each study using GenomeStudio with the GenCall 2.0 algorithm. Samples were called using study-specific cluster definitions (based on samples with call rate >95%, ARIC, MEC, WHI) or cluster definitions provided by Illumina (GenNet, HyperGEN) and kept in the analysis if call rate was >95%. We excluded SNPs with GenTrain score <0.6 (ARIC, MEC, WHI) or <0.7 (GenNet, HyperGEN), cluster separation score <0.4, call rate <0.95, and Hardy-Weinberg Equilibrium p<1×10−6. We also excluded SNPs based on Mendelian errors in 30 YRI trios >1, replication errors >2 with discordant calls (when comparing across studies) in 90 YRI samples >3, and discordant calls for 90 YRI genotyped in PAGE versus HapMap database >3. In
