FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also...

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Autores principales: Sboner, Andrea, Habegger, Lukas, Pflueger, Dorothee, Terry, Stephane, Chen, David Z, Rozowsky, Joel S, Tewari, Ashutosh K, Kitabayashi, Naoki, Moss, Benjamin J, Chee, Mark S, Demichelis, Francesca, Rubin, Mark A, Gerstein, Mark B
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218660/
https://www.ncbi.nlm.nih.gov/pubmed/20964841
http://dx.doi.org/10.1186/gb-2010-11-10-r104
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author Sboner, Andrea
Habegger, Lukas
Pflueger, Dorothee
Terry, Stephane
Chen, David Z
Rozowsky, Joel S
Tewari, Ashutosh K
Kitabayashi, Naoki
Moss, Benjamin J
Chee, Mark S
Demichelis, Francesca
Rubin, Mark A
Gerstein, Mark B
author_facet Sboner, Andrea
Habegger, Lukas
Pflueger, Dorothee
Terry, Stephane
Chen, David Z
Rozowsky, Joel S
Tewari, Ashutosh K
Kitabayashi, Naoki
Moss, Benjamin J
Chee, Mark S
Demichelis, Francesca
Rubin, Mark A
Gerstein, Mark B
author_sort Sboner, Andrea
collection PubMed
description We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements.
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spelling pubmed-32186602011-11-18 FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data Sboner, Andrea Habegger, Lukas Pflueger, Dorothee Terry, Stephane Chen, David Z Rozowsky, Joel S Tewari, Ashutosh K Kitabayashi, Naoki Moss, Benjamin J Chee, Mark S Demichelis, Francesca Rubin, Mark A Gerstein, Mark B Genome Biol Method We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements. BioMed Central 2010 2010-10-21 /pmc/articles/PMC3218660/ /pubmed/20964841 http://dx.doi.org/10.1186/gb-2010-11-10-r104 Text en Copyright ©2010 Sboner et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Sboner, Andrea
Habegger, Lukas
Pflueger, Dorothee
Terry, Stephane
Chen, David Z
Rozowsky, Joel S
Tewari, Ashutosh K
Kitabayashi, Naoki
Moss, Benjamin J
Chee, Mark S
Demichelis, Francesca
Rubin, Mark A
Gerstein, Mark B
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
title FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
title_full FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
title_fullStr FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
title_full_unstemmed FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
title_short FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
title_sort fusionseq: a modular framework for finding gene fusions by analyzing paired-end rna-sequencing data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218660/
https://www.ncbi.nlm.nih.gov/pubmed/20964841
http://dx.doi.org/10.1186/gb-2010-11-10-r104
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