Genome-wide gene expression data were obtained from 805 Dutch individuals (357 patients and 448 controls), who were also genotyped on either the HumanHap 300K, HumanCNV 370K or HumanHap 550K platforms in the previously described GWAS [7]. Patients were recruited at our referral clinic for motor neuron disease at the University Medical Center Utrecht, The Netherlands. Included patients were diagnosed with probable or definite sporadic ALS according to the 1994 El Escorial criteria [27]. Messenger RNA was collected and extracted from peripheral whole blood using PAXgene tubes and PAXgene extraction kit (Qiagen). Samples were hybridized to Illumina HumanHT-12v3 Expression BeadChips. Case and control samples were randomly assigned to the chips and all chips were run in one batch. Before quality control, expression levels were available for 48,803 probes. Raw expression data were quantile normalized and log2 transformed [30] in R (2009, The R Foundation for Statistical Computing). Using principal components analysis of expression data, outlier arrays were detected. Non-pseudoautosomal Y chromosome transcript expression levels were used for a gender check. Outlier arrays, samples with inconsistent gender information, and samples designated as
