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JAFFAL: detecting fusion genes with long-read transcriptome sequencing.

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 .

SUBMITTER: Davidson NM

PROVIDER: S-EPMC8739696 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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JAFFAL: detecting fusion genes with long-read transcriptome sequencing.

Davidson Nadia M NM Chen Ying Y Sadras Teresa T Ryland Georgina L GL Blombery Piers P Ekert Paul G PG Göke Jonathan J Oshlack Alicia A

Genome biology 20220106 1

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 ...[more]

PMID: 34991664

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