Yale-Penn GWAS samples were genotyped on the Illumina HumanOmni1-Quad v1.0 microarray, including 988,306 autosomal single nucleotide polymorphisms (SNPs; Illumina, San Diego, California), at the Center for Inherited Disease Research and the Yale Center for Genome Analysis. Genotypes were called using GenomeStudio software V2011.1 and genotyping module V1.8.4 (Illumina, San Diego, California). SAGE samples were genotyped on the Illumina Human 1M array containing 1,069,796 total SNPs (Illumina). In the Yale-Penn GWAS dataset, 44,644 SNPs on the microarray and 135 individuals with call rates <98% were excluded; 62,076 additional SNPs were removed due to minor allele frequencies (MAF) <1%. After data cleaning and quality control, 5697 individuals and 889,659 SNPs remained for imputation. Additional quality control information has been reported previously (1). After applying the same quality control procedures to the SAGE sample, 39 subjects with call rates <98% were excluded and 726,191 SNPs remained for analysis.
