A recent alternative to gene expression profiling with microarrays is RNA-seq, in which RNA is sequenced with one the new high-throughput sequencing (HTS) platforms. Typically, several hundred millions of short sequence reads are generated in such an experiment, which allows an unbiased estimate of the number of copies for each transcript. An advantage of RNA-seq compared to microarrays is that they can detect previously uncharacterized transcripts (small non-coding RNAs, microRNAs,…) because it doesn’t rely on predefined sets of probes. Additionally, the sequence itself can be used to detect potentially oncogenic mutations or other functionally important sequence variants. Some complications with these data are their sheer volume and the relatively short length of the sequence that sometimes makes unambiguous mapping of their position in the genome impossible. Targeted sequencing is a related technique that uses selection of specific genomic regions or genes before sequencing, allowing focusing on these regions.
A representative platform for high-throughput sequencing is the Illumina HiSeq 2000 platform which can generate in about ten days up to 600GB of sequence data consisting of paired-end reads of 100bp.
