Measuring ASE needs the clear identification of the two different alleles in the F1 hybrid and relies on the presence of sequence polymorphisms within the transcribed sequence.
We and others proposed methods to have a global analysis of the genome using DNA-arrays (Kiekens et al. 2006) or SNP-arrays (Bjornsson et al. 2008, Ronald et al. 2005, Zhang and Borevitz 2009). One disadvantage of SNP-arrays is that only known SNPs can be detected. Furthermore, the hybridization properties of microarrays complicates the assessment of the presence of one SNP among another. Therefore, next-generation sequencing technology (NGST) is more convenient for ASE as it allows SNP detection and allele distinction in diploids by giving the true sequence of the transcript with no prior information about the sequence. We (Naouar et al. manuscript in preparation) recently developed a pipline to measure and identify genome-wide ASE using Roche 454 NGST.