Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

Lynnette Fernandez-Cuesta; Ruping Sun; Roopika Menon; Julie George; Susanne Lorenz; Leonardo A. Meza-Zepeda; Martin Peifer; Dennis Plenker; Johannes M. Heuckmann; Frauke Leenders; Thomas Zander; Ilona Dahmen; Mirjam Koker; Jakob Schöttle; Roland T. Ullrich; Janine Altmüller; Christian Becker; Peter Nürnberg; Henrik Seidel; Diana Böhm; Friederike Göke; Sascha Ansén; Prudence A. Russell; Gavin M. Wright; Zoe Wainer; Benjamin Solomon; Iver Petersen; Joachim H. Clement; Jörg Sänger; Odd Terje Brustugun; Åslaug Helland; Steinar Solberg; Marius Lund-Iversen; Reinhard Buettner; Jürgen Wolf; Elisabeth Brambilla; Martin Vingron; Sven Perner; Stefan A. Haas; Roman K. Thomas

doi:10.1186/s13059-014-0558-0

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

Lynnette Fernandez-Cuesta, Ruping Sun, Roopika Menon, Julie George, Susanne Lorenz, Leonardo A. Meza-Zepeda, Martin Peifer, Dennis Plenker, Johannes M. Heuckmann, Frauke Leenders, Thomas Zander, Ilona Dahmen, Mirjam Koker, Jakob Schöttle, Roland T. Ullrich, Janine Altmüller, Christian Becker, Peter Nürnberg, Henrik Seidel, Diana BöhmFriederike Göke, Sascha Ansén, Prudence A. Russell, Gavin M. Wright, Zoe Wainer, Benjamin Solomon, Iver Petersen, Joachim H. Clement, Jörg Sänger, Odd Terje Brustugun, Åslaug Helland, Steinar Solberg, Marius Lund-Iversen, Reinhard Buettner, Jürgen Wolf, Elisabeth Brambilla, Martin Vingron, Sven Perner, Stefan A. Haas^*, Roman K. Thomas

^*Corresponding author for this work

Institute of Pathology

32 Citations (Scopus)

Abstract

Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline) (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondary rearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.

Original language	English
Article number	7
Journal	Genome Biology
Volume	16
Issue number	1
ISSN	1474-7596
DOIs	https://doi.org/10.1186/s13059-014-0558-0
Publication status	Published - 05.01.2015

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Fernandez-Cuesta, L., Sun, R., Menon, R., George, J., Lorenz, S., Meza-Zepeda, L. A., Peifer, M., Plenker, D., Heuckmann, J. M., Leenders, F., Zander, T., Dahmen, I., Koker, M., Schöttle, J., Ullrich, R. T., Altmüller, J., Becker, C., Nürnberg, P., Seidel, H., ... Thomas, R. K. (2015). Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. Genome Biology, 16(1), Article 7. https://doi.org/10.1186/s13059-014-0558-0

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abstract = "Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline) (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondary rearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.",

author = "Lynnette Fernandez-Cuesta and Ruping Sun and Roopika Menon and Julie George and Susanne Lorenz and Meza-Zepeda, {Leonardo A.} and Martin Peifer and Dennis Plenker and Heuckmann, {Johannes M.} and Frauke Leenders and Thomas Zander and Ilona Dahmen and Mirjam Koker and Jakob Sch{\"o}ttle and Ullrich, {Roland T.} and Janine Altm{\"u}ller and Christian Becker and Peter N{\"u}rnberg and Henrik Seidel and Diana B{\"o}hm and Friederike G{\"o}ke and Sascha Ans{\'e}n and Russell, {Prudence A.} and Wright, {Gavin M.} and Zoe Wainer and Benjamin Solomon and Iver Petersen and Clement, {Joachim H.} and J{\"o}rg S{\"a}nger and Brustugun, {Odd Terje} and {\AA}slaug Helland and Steinar Solberg and Marius Lund-Iversen and Reinhard Buettner and J{\"u}rgen Wolf and Elisabeth Brambilla and Martin Vingron and Sven Perner and Haas, {Stefan A.} and Thomas, {Roman K.}",

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Fernandez-Cuesta, L, Sun, R, Menon, R, George, J, Lorenz, S, Meza-Zepeda, LA, Peifer, M, Plenker, D, Heuckmann, JM, Leenders, F, Zander, T, Dahmen, I, Koker, M, Schöttle, J, Ullrich, RT, Altmüller, J, Becker, C, Nürnberg, P, Seidel, H, Böhm, D, Göke, F, Ansén, S, Russell, PA, Wright, GM, Wainer, Z, Solomon, B, Petersen, I, Clement, JH, Sänger, J, Brustugun, OT, Helland, Å, Solberg, S, Lund-Iversen, M, Buettner, R, Wolf, J, Brambilla, E, Vingron, M, Perner, S, Haas, SA & Thomas, RK 2015, 'Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data', Genome Biology, vol. 16, no. 1, 7. https://doi.org/10.1186/s13059-014-0558-0

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T1 - Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

AU - Fernandez-Cuesta, Lynnette

AU - Sun, Ruping

AU - Menon, Roopika

AU - George, Julie

AU - Lorenz, Susanne

AU - Meza-Zepeda, Leonardo A.

AU - Peifer, Martin

AU - Plenker, Dennis

AU - Heuckmann, Johannes M.

AU - Leenders, Frauke

AU - Zander, Thomas

AU - Dahmen, Ilona

AU - Koker, Mirjam

AU - Schöttle, Jakob

AU - Ullrich, Roland T.

AU - Altmüller, Janine

AU - Becker, Christian

AU - Nürnberg, Peter

AU - Seidel, Henrik

AU - Böhm, Diana

AU - Göke, Friederike

AU - Ansén, Sascha

AU - Russell, Prudence A.

AU - Wright, Gavin M.

AU - Wainer, Zoe

AU - Solomon, Benjamin

AU - Petersen, Iver

AU - Clement, Joachim H.

AU - Sänger, Jörg

AU - Brustugun, Odd Terje

AU - Helland, Åslaug

AU - Solberg, Steinar

AU - Lund-Iversen, Marius

AU - Buettner, Reinhard

AU - Wolf, Jürgen

AU - Brambilla, Elisabeth

AU - Vingron, Martin

AU - Perner, Sven

AU - Haas, Stefan A.

AU - Thomas, Roman K.

PY - 2015/1/5

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N2 - Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline) (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondary rearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.

AB - Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline) (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondary rearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.

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DO - 10.1186/s13059-014-0558-0

M3 - Journal articles

C2 - 25650807

AN - SCOPUS:84939129092

SN - 1474-7596

VL - 16

JO - Genome Biology

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Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

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