Systematic Identification of Novel Fusion Transcripts

Fusion transcripts are products of chromosomal rearrangements that are frequently involved in carcinogenesis. A genomic translocation event can result in the fusion of two genes. The resulting chimeric gene is transcribed into a fusion transcript which in turn is translated into a fusion protein. In order to identify fusion transcripts systematically and comprehensively, we developed a pipeline that uses the sequence alignment tool Splign to analyze mRNA sequences. We benchmarked our alignment results against well characterized fusion transcripts and tuned the alignment criteria to minimize false positives and false negative signals. Using this approach, we analyzed the entire set of human Genbank mRNAs (~250,000 accessions) on the human genome. From analyzing the alignment results, we were able to identify 1054 novel fusion transcripts that have not been described before, 260 of which have high level confidence with more stringent criteria. The newly identified fusion transcripts can be valuable for cancer research.