![]() Detecting gene fusion from RNA-seq short reads is a very active research area, with novel methods being published regularly (e.g. for a recent review focusing on gene fusions in cancer, showing that mapping-based methods generally outperform assembly-based methods. These tools use approaches based on either reads mapping or assembly. Gene fusion discovery with short paired-end reads is a well-studied problem and many tools have been developed to address it. ![]() Traditionally gene fusion discovery is done using short reads generated by Illumina sequencing. All this underscores the importance of detecting accurately gene fusions. Moreover, gene fusions are not specific to cancer and are also important for other diseases. Several studies suggest that recurrent gene fusions can be used as potential biomarkers in cancer. This fusion is observed in ∼50 % of prostate cancer patients and is associated with high expression of estrogen regulated gene (ERG). TMPRSS2-ERG is one of such fusions created by the deletion of ∼2.8Mb between these genes. Gene fusions between androgen regulated genes and genes from the ETS family are observed in many prostate cancer patients. This gene fusion causes genome instability and impairs signaling pathways. For example, the BCR-ABL1 fusion, caused by a balanced reciprocal translocation between chromosomes 9 and 22, is observed in chronic myeloid leukemia. Gene fusions are observed in many types of cancer. for a detailed discussion on gene fusions and chimeric RNAs. Gene fusions may hinder the original functions of the fused genes and can introduce functional novelty. Gene fusions are aberrations that result from genomic events such as deletions, inversions or translocations, whereby segments of two genes become closely located and are transcribed together into a chimeric RNA molecule. Genion is implemented in C++ and is available at. Genion is an accurate gene fusion caller. Furthermore, our results on the breast cancer cell line MCF-7 show that Genion correctly identifies all the experimentally validated gene fusions. On simulated data, Genion accurately identifies the gene fusions and its clustering accuracy for detecting fusion reads is better than LongGF. We compare Genion against a recently introduced long-read gene fusion discovery method, LongGF, both on simulated and real datasets. We present Genion, a sensitive and fast gene fusion detection method that can also detect read-through events. Transcriptomic long-read sequencing presents unique opportunities to overcome the shortcomings of short-read technologies for gene fusion detection while introducing new challenges. Advances in long-read sequencing technologies allow the generation of long transcriptomics reads at a low cost. But the sensitivity of these methods is limited by the technology, especially the short read length. Gene fusion discovery with short reads is a well-studied problem, and many methods have been developed. These chimeric transcripts are also known as read-through and trans-splicing transcripts. This is different from fusion transcripts created during or after the transcription process. Gene fusions are the result of structural genomic events that bring two genes closely located and result in a fused transcript. A widely studied topic is gene fusion which is observed in many cancer types and suspected of having oncogenic properties. The advent of next-generation sequencing technologies empowered a wide variety of transcriptomics studies.
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