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Chunk #36 — Materials and Methods — Initial genomic mapping of Illumina expression probe sequences

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Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA.
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(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, if multiple hits were present whether all these mappings resided in each other vicinity (<250 kb). Probes that did not map at all, or mapped to multiple different loci were excluded from further analyses. Using this approach, 43,202 of the 48,751 probes on the HT12 and 21,316 of the 22,185 probes on the H8v2 platform were eventually mapped to a single genomic location.