JAFFAL: detecting fusion genes with long-read transcriptome sequencing
- Author(s)
- Davidson, NM; Chen, Y; Sadras, T; Ryland, GL; Blombery, P; Ekert, PG; Goke, J; Oshlack, A;
- Journal Title
- Genome Biology
- Publication Type
- Research article
- Abstract
- In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of fusions with their full-length isoform structure. However, due to higher sequencing error rates, fusion finding algorithms designed for short reads do not work. Here we present JAFFAL, to identify fusions from long-read transcriptome sequencing. We validate JAFFAL using simulations, cell lines, and patient data from Nanopore and PacBio. We apply JAFFAL to single-cell data and find fusions spanning three genes demonstrating transcripts detected from complex rearrangements. JAFFAL is available at https://github.com/Oshlack/JAFFA/wiki .
- Keywords
- Algorithms; Gene Fusion; *High-Throughput Nucleotide Sequencing; Humans; Sequence Analysis, DNA; *Transcriptome; Fusions; Long reads; Nanopore; PacBio; RNA sequencing; Translocations
- Department(s)
- Laboratory Research; Pathology; Haematology
- PubMed ID
- 34991664
- Publisher's Version
- https://doi.org/10.1186/s13059-021-02588-5
- Open Access at Publisher's Site
https://doi.org/10.1186/s13059-021-02588-5- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2024-10-18 06:46:45
Last Modified: 2024-10-18 06:47:15