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The most significant imputed SNP was individually genotyped in a subset of cases using standard protocols for the Fluidigm BioMark™ HD System (Fluidigm, South San Francisco, CA, USA) (Supplementary Material, Information) to confirm imputation accuracy, resulting in 99% concordance between the genotyped and imputed genotypes.
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For a gene region that contains the most significant finding, we imputed genotype data for all SNPs reported in the 1000 Genomes project [ 35].
To determine independent signals within imputed SNPs at STAT3, we ran a stepwise forward multiple logistic regression model including the most significant genotyped SNP rs1905339 and all imputed SNPs, adjusted for study, age and 16 PCs.
For SNPs imputed across all three studies, we selected the most significant SNP associated with type 2 diabetes.
To explore ungenotyped SNPs that might be functional, we imputed SNPs surrounding the selected genes (+/−200 kb) harboring or close to the most significant SNP loci using 1000 Genomes data as a reference (Additional file 1: Figure S1A, B, and C).
Daetwyler et al. [ 22] also pointed out that results of association studies that are based on imputed sequences should be interpreted with caution, since SNPs with slightly higher P values than the most significant SNPs from multiple-testing can also be considered as potential causative mutations, particularly if there is strong supporting functional evidence.
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