Genome-wide SNP genotyping was performed within each cohort using Illumina or Affymetrix genotyping arrays. Follow-up (“Stage II”) genotyping of selected variants was performed using a custom content on the Illumina Human Exome array. Details of genotyping and QC are provided in Supplementary Material (Section C in S1 File ); these procedures generally involved exclusion of participants on the basis of sex mismatches and duplicate samples; limitation to unrelated individuals in all cohorts except the family-based FHS; exclusion of samples with genotyping success rate <95%; and exclusion of SNPs failing genotyping call rate thresholds, typically between 95% and 99%.
To increase coverage and facilitate evaluation of the same SNPs across cohorts, SNPs passing quality control were used to impute to the HapMap Phase 2 reference panels using MaCH [17 (link)], BEAGLE, [18 (link)] or BIMBAM [19 (link)].
To increase coverage and facilitate evaluation of the same SNPs across cohorts, SNPs passing quality control were used to impute to the HapMap Phase 2 reference panels using MaCH [17 (link)], BEAGLE, [18 (link)] or BIMBAM [19 (link)].
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