Various mapping strategies were used for the expression probes to get a mapping location that was as unambiguous as possible: if probes have been mapped incorrectly, or cross-hybridize to multiple genomic loci, it might be that an eQTL will be incorrectly deemed a trans-eQTL, while in fact it is a cis-eQTL or primer polymorphisms. We used Ensembl database version 52 (NCBI 36.3 assembly) to obtain, for each annotated gene, the transcript with the largest number of exons and included this main spliced transcript in our reference set. Second, we added one sequence per intron, extending intron boundaries 40 bp on each side to allow mapping of the 50 bp probe sequences that overlapping exon-intron junctions. Last, a version of the reference DNA genome with masked annotated transcripts was included. Probe sequences were mapped using NOVOALIGN V2.05.12 for all the sequences (main transcript, introns, and non standard exon-exon junctions) originating from the same transcript (parameters −t 150 −v 20 20 200 [>]( [ ^_]*)_). For each probe it was determined whether it was mapping uniquely to one particular genomic locus, or,
