The strengths of our study are the meticulous pruning of expression probes as present on the expression array, with regard to non-specific mapping in the human transcriptome, or harboring SNPs that might interfere with hybridization of probes to the array, resulting in false-positive eQTLs [33]. In addition, permutation schemes were applied, preserving the LD structure within subjects, also minimizing the detection of false-positive eQTLs. Finally, a two-stage approach, both for eQTLs discovery purposes and for the detection of novel SNP-ALS associations, ensures robustness of the results.
