Fig. 1: Schematics of the THISTLE sQTL analysis.
From: Genetic control of RNA splicing and its distinct role in complex trait variation
In this toy example, a genetic variant with two alleles, G and A, is associated with a splicing event (for example, exon skipping) in a gene with two transcript isoforms, T1 and T2. a,b, Schematics of the THISTLE sQTL analysis in the absence of an eQTL effect. In this scenario, individuals with the G allele show higher mean abundance of T1 than T2 and individuals with the A allele show higher mean abundance of T2 than T1 (a), meaning that the genetic variant is associated with the difference in abundance between isoforms. In other words, there is a difference in the isoform-eQTL effect between T1 and T2 (b). However, there is no difference in overall gene expression between individuals with different alleles, meaning that this genetic variant is not an eQTL. c,d, Schematics of the THISTLE sQTL analysis in the presence of an eQTL effect. In this scenario, individuals with the G allele show similar abundance between T1 and T2 and individuals with the A allele show lower abundance of T1 than T2 (c). The isoform-eQTL effect for T1 is different from that for T2 albeit in the same direction (d). In this case, there is a difference in overall gene expression between alleles G and A, meaning that this genetic variant is also an eQTL.
