Chunk #49 — 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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We also assessed whether any of the Illumina SNPs that constitute trans-eQTLs might map to a different position than what is reported in dbSNP. As such we mapped the 50 bp Illumina SNP probe sequences to the genome assembly, permitting up to four mismatches per 50 bp SNP probe sequence. We did not observe any SNP that could map (with some mismatches) to the same chromosome of the trans-probe.