Transcriptomics

Blood samples for the collection of gene expression data were taken at study baseline. Transcriptional profiling was performed in two batches using the Illumina HumanHT-12 v3 (batch one) and v4 (batch two) Expression BeadChip kits. Original raw data can be found in GEO¹. Preprocessed raw data files, as well as post quality control, batch corrected expression values, are distributed via Synapse. The processed data underwent background correction, log base two transformation and all values were robust spline normalized [18]. Outlying samples were excluded. Batch correction was performed using ComBat [19]. All data were subset to probes that could reliably be detected in at least 80%of samples in at least one diagnostic group. More details on the processing of the data is explained in Voyle et al. [18].