Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies

Abstract

RNA sequencing (RNA-seq) is the current gold-standard method to quantify gene expression for eQTL studies. However, a potential caveat in these studies is that RNA-seq reads carrying the nonreference allele of variant loci can have lower probability to map correctly to the reference genome, which could bias gene quantifications and cause false positive eQTL associations. In this study, we analyze the effect of this allelic mapping bias in eQTL discovery. PMID: 25239376