RNA-seq is the application of next generation sequencing to survey the content of the transcriptome (54). It is a step up from previously applied sequencing methods for gene expression like SAGE (56). It can provide a quantitative assessment of transcription including sequence information across the transcriptome. That allows the identification and assessment of normal or disease–causing alternative splicing, the discovery of coding variation including pathogenic mutations, and the assessment of allele-specific expression differences revealed by transcribed polymorphisms. It is clear that in the study of disease this approach has significant advantages over hybridization-based microarray analysis.
