Prior studies unambiguously demonstrate that inherited variation is a determinant of gene expression (Cheung et al., 2003; Montgomery et al., 2010; Pickrell et al., 2010; Schadt et al., 2003; Stranger et al., 2005). Polymorphisms associated with mRNA levels are typically referred to as expression quantitative trait loci (eQTLs). eQTL studies have shed light on the genetic architecture of gene expression. eQTLs have also provided key insights into genes and pathways underlying the associations by providing an intermediate phenotype between non-protein coding genetic variants and complex traits (Chen et al., 2008; Cookson et al., 2009; Emilsson et al., 2008; Grisanzio et al., 2012; Musunuru et al., 2010; Pomerantz et al., 2009). In fact, trait-associated loci are enriched for eQTLs (Nicolae et al., 2010). Most of our knowledge, however, is based on data derived from cell lines and normal tissues (Dimas et al., 2009; Myers et al., 2007; Nica et al., 2010). By contrast, cancer studies typically generate more expression data on tumors than in normal tissues.
