Mismapping of sequencing reads from polymorphic duplications generates spurious trans-eQTLs

Polymorphic gene duplications absent from the reference genome can generate spurious trans-eQTLs. Specifically, variants tagging the polymorphic duplicate may masquerade as trans-eQTLs regulating the reference gene copy. Here, we develop a method to identify these artifacts in trans-eQTL maps using apparent linkage disequilibrium between putative trans-eQTLs and their target genes.