Around 21,000 individuals across the cohorts have been typed using Metabochip (see Table 4 ), a genotyping platform consisting of ∼200,000 SNPs, which cover the loci identified by GWAS in cardiometabolic diseases, and rare variants from the 1000 Genomes Project [23] (link). This will be supplemented by SNP data from a whole genome array in the 1958 Birth Cohort, the 50 k HumanCVD Beadchip [37] (link) in WHII and BWHHS, and prior candidate and GWAS replication work in all studies. The NPHS-II, EHDPS and AAAT studies are available for new bespoke genotyping e.g. to validate associations from UCLEB samples genotyped by Metabochip. This will yield a powerful aggregate dataset rich in genetic and phenotypic detail.
Duplicate samples have been genotyped to compute the error rate. Initial quality control analysis on genotyped data identified any problem samples that have been subsequently excluded in further analysis. These included: checks for discordance between reported and genetically-determined ethnicity, replicate concordance, sample mix-up (unknown duplicates and comparison to previously genotyped data where available), gender ambiguity and cryptic relatedness (seeFigure S1 ).
Duplicate samples have been genotyped to compute the error rate. Initial quality control analysis on genotyped data identified any problem samples that have been subsequently excluded in further analysis. These included: checks for discordance between reported and genetically-determined ethnicity, replicate concordance, sample mix-up (unknown duplicates and comparison to previously genotyped data where available), gender ambiguity and cryptic relatedness (see
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