Gene Fusion Detection – more complex than you might assume

Gene Fusion Detection – more complex than you might assume

Abstract
Gene fusions, which occur when two previously separate genes become joined together, can result in the formation of abnormal proteins and have been implicated in various human diseases such as cancer. Detection of gene fusions is a crucial step in understanding the underlying biology of these diseases and in developing new diagnostic and therapeutic approaches.
Next-generation sequencing (NGS) technologies have revolutionized the field of gene fusion detection by providing a high-throughput and cost-effective method for identifying these genetic events. The split-read method takes advantage of the fact that during the sequencing process, when a fusion occurs between two genes, the resulting chimeric RNA molecule or the rearranged genomic DNA fragment is sequenced in one contiguous step. Aligning these reads, that are spanning fusion junctions, to the reference genome results in so-called split-reads where different parts map to different genomic locations.
However, this split-read method for detecting fusion events is not without limitations. It relies on the presence of at least some split-reads for each gene fusion, which may not always be the case, particularly for low-frequency or lowly expressed fusions. Furthermore, the approach can be prone to false-positive calls, which can be caused by various factors such as sequencing errors and annotation errors.