Chunk #48 — 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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Using this strategy we observed several instances where only 20 out the 50 bases of a probe sequence mapped in the vicinity of the trans-SNP (data not shown). For these trans-eQTLs the Spearman's rank correlation p was often lower than 10−100, which would imply these SNPs explain over 25% of the total expression variation of the corresponding trans-genes. Given the small amount of trans-eQTLs we detected in total, such effect sizes are quite unlikely and therefore provide circumstantial evidence these indeed reflect cross-hybridization artifacts.