Chinnaiyan and colleagues have combined 454 and Solexa sequencing to identify transcripts resulting from gene fusion, both in cancer cell lines and primary tumors. The approach relies on deep sequencing the cancer transcriptome and looking for reads that show partial alignment to exon boundaries from different genes. When applied to prostate cancer cell lines and tumors, it detects the well-known TMPRSS-ERG fusion but also discover several novel fusions. It is likely that this approach will lead to the discovery of many novel oncogenes in the near future.
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature07638.html
