JAFFAL: detecting fusion genes with long-read transcriptome sequencing

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. Her...

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Autores principales: Davidson, Nadia M., Chen, Ying, Sadras, Teresa, Ryland, Georgina L., Blombery, Piers, Ekert, Paul G., Göke, Jonathan, Oshlack, Alicia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8739696/
https://www.ncbi.nlm.nih.gov/pubmed/34991664
http://dx.doi.org/10.1186/s13059-021-02588-5
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author Davidson, Nadia M.
Chen, Ying
Sadras, Teresa
Ryland, Georgina L.
Blombery, Piers
Ekert, Paul G.
Göke, Jonathan
Oshlack, Alicia
author_facet Davidson, Nadia M.
Chen, Ying
Sadras, Teresa
Ryland, Georgina L.
Blombery, Piers
Ekert, Paul G.
Göke, Jonathan
Oshlack, Alicia
author_sort Davidson, Nadia M.
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02588-5.
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spelling pubmed-87396962022-01-07 JAFFAL: detecting fusion genes with long-read transcriptome sequencing Davidson, Nadia M. Chen, Ying Sadras, Teresa Ryland, Georgina L. Blombery, Piers Ekert, Paul G. Göke, Jonathan Oshlack, Alicia Genome Biol Method 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02588-5. BioMed Central 2022-01-06 /pmc/articles/PMC8739696/ /pubmed/34991664 http://dx.doi.org/10.1186/s13059-021-02588-5 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Davidson, Nadia M.
Chen, Ying
Sadras, Teresa
Ryland, Georgina L.
Blombery, Piers
Ekert, Paul G.
Göke, Jonathan
Oshlack, Alicia
JAFFAL: detecting fusion genes with long-read transcriptome sequencing
title JAFFAL: detecting fusion genes with long-read transcriptome sequencing
title_full JAFFAL: detecting fusion genes with long-read transcriptome sequencing
title_fullStr JAFFAL: detecting fusion genes with long-read transcriptome sequencing
title_full_unstemmed JAFFAL: detecting fusion genes with long-read transcriptome sequencing
title_short JAFFAL: detecting fusion genes with long-read transcriptome sequencing
title_sort jaffal: detecting fusion genes with long-read transcriptome sequencing
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8739696/
https://www.ncbi.nlm.nih.gov/pubmed/34991664
http://dx.doi.org/10.1186/s13059-021-02588-5
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