With the advance of the next-generation sequencing technologies, RNA-seq

has become a useful tool in defining the transcriptomes of cells with the

advantage of analyzing expression at exon levels as well as delineating novel

splicing variants[10, 11]. Early application of RNA-seq included expression

profiling of yeast[12], mouse brain, liver and skeletal muscle tissues[13], human

embryonic kidney and a B cell line[14]. RNA-seq has several advantages over

other expression profiling technologies including higher sensitivity, ability to

detect splicing isoforms and somatic mutations[11]. For cancer expression

profiling, Berger et al. applied RNA-seq to expression profiling of melanoma

[15]. They identified 11 novel melanoma gene fusions and 12 novel

read-through transcripts, providing an example of novel avenues for target

discovery in cancers. To date, the RNA-seq analysis of HBV-related HCC has

not been published. We therefore applied RNA-seq technology to analyze 10

matched pairs of HCC tissues and their adjacent non-cancerous tissues.