Subjects are designated as Yale-Penn 1, 2, and 3 by the recruitment epoch and microarray platform used for genotyping. Samples for Yale-Penn 1 (n=5540) were genotyped on the Illumina (San Diego, CA, USA) HumanOmni1-Quad v1.0 microarray at the Center for Inherited Disease Research and the Yale Center for Genome Analysis. A total of ∼1M SNPs were targeted by microarray in Yale-Penn 1. Samples for Yale-Penn 2 (n=3675) were genotyped with the Illumina HumanCore Exome array, which includes a total of ∼0.5M SNPs, including exomic SNPs and tagging SNPs. Genotyping in Yale-Penn 3 (n=592) was performed with the Illumina Multi-Ethnic Genotyping Array, an array targeting ∼1.7M genome-wide markers and optimized for GWAS in populations of diverse ancestries. Yale-Penn 2 and Yale-Penn 3 genotyping data were obtained at the Gelernter Lab at Yale. Quality control (QC) for microarrays in each cohort were carried out using PLINK1.9 (5) based on the following criteria: (1) an individual genotype missing rate <2%, (2) a SNP genotype missing rate <2%, (3) a Hardy-Weinberg P>1×10-6, and (4) a minor allele frequency (MAF) >1%. After QC, there were ∼0.70M, ∼0.27M, and ∼1.1M SNPs remaining in Yale-Penn 1-3 respectively, which were subjected to imputation and downstream analysis.
