Illumina Gene Expression Data Processing

In the KORA F4 study, the preparation of gene expression data on the Illumina HumanHT-12 v3 expression BeadChip was performed as described previously [36] (link). Gene expression data are available for download at ArrayExpress (E-MTAB-1708). All KORA F4 samples were genotyped using the Affymetrix 6.0 GeneChip. We limited our analysis to SNPs with a minor allele frequency >5% and a high genotyping quality (call rate >95%) and with respect to Hardy-Weinberg equilibrium (P_HWE > 1E-6). 616,941 SNPs fulfilled all these criteria. The preparation of the KORA F4 samples as well as of the SHIP-TREND and EGCUT samples is described in Table 1 to indicate the differences and similarities between the three studies.