In the Rotterdam Study, RNA was isolated from whole blood and gene expression profiling was performed using the IlluminaHumanHT-12v4 Expression Beadchips (Illumina, San Diego, CA, USA). The expression dataset is available at Gene Expression Omnibus (GEO) public repository under the accession GSE33828: 881 samples are available for analysis. In KORA F4, total RNA was extracted from whole blood and the Illumina Human HT-12 v3 Expression BeadChip (Illumina, San Diego, CA, USA) was used for gene expression profiling [59 (link)]. A more detailed description is implemented in Additional file 8 .
In the current study, genes of interest were selected using a previous TWAS testing the association between gene expression and current versus never-smoking status [8 (link)]. In this TWAS, the meta-analysis was performed on all transcripts with matching gene Entrez IDs. Employing a significance threshold of FDR < 0.05, 886 significant gene Entrez IDs were identified, of which 387 replicated in an independent dataset. Employing the annotation file provided by the Illumina (HumanHT-12_V4), we found 502 gene expression probes to be annotated to these gene Entrez IDs out of which 443 were present in the Rotterdam Study and were included in the current study (Additional file8 : Table S9).
In the current study, genes of interest were selected using a previous TWAS testing the association between gene expression and current versus never-smoking status [8 (link)]. In this TWAS, the meta-analysis was performed on all transcripts with matching gene Entrez IDs. Employing a significance threshold of FDR < 0.05, 886 significant gene Entrez IDs were identified, of which 387 replicated in an independent dataset. Employing the annotation file provided by the Illumina (HumanHT-12_V4), we found 502 gene expression probes to be annotated to these gene Entrez IDs out of which 443 were present in the Rotterdam Study and were included in the current study (Additional file
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