There is growing evidence that allele-specific differences in gene expression, arising from cis-acting regulatory polymorphisms, are an important source of phenotypic variability, including susceptibility to complex disorders (Bray et al., 2003; Sadee, 2009). Allelic imbalance is a robust and accurate tool to identify cis-regulatory variation while minimizing confounding trans-acting factors, including tissue preparation methods and post-mortem interval as well as trans-acting genetic events (Bray and O'Donovan, 2006; Pastinen and Hudson, 2004; Stamatoyannopoulos, 2004; Yan and Zhou, 2004). Allelic differences in expression appear to be context specific, for example, with regard to tissue-type, and the effects of cis-regulatory polymorphism on gene expression can differ widely between tissues (Sun et al., 2010; Wilkins et al., 2007; Zhang et al., 2009). Moreover, differential allelic expression across multiple regions of the adult human brain has been reported (Buonocore et al., 2010). Therefore, it's important that ASE analysis focuses on relevant target tissues.
