Chunk #50 — Materials and Methods — Identification of false eQTLs due to primer polymorphisms and cross-hybridization

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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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It is still possible that some of the trans-eQTLs for which we did not find any evidence of cross-hybridization, still are false positives, e.g. by missing some cross-hybridizations due to imperfections in the NCBI v36 assembly we used. Although we have identified numerous occasions where a SNP affects two different probes within the same gene in trans, substantiating the likelihood these trans-eQTLs are real, providing unequivocal evidence that all our reported trans-eQTLs are real is not straightforward.