Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data
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 R...
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| Veröffentlicht in: | Genome Biology 2015-01, Vol.16 (1), p.7-7, Article 7 |
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| creator | Fernandez-Cuesta, Lynnette Sun, Ruping Menon, Roopika George, Julie Lorenz, Susanne Meza-Zepeda, Leonardo A Peifer, Martin Plenker, Dennis Heuckmann, Johannes M Leenders, Frauke Zander, Thomas Dahmen, Ilona Koker, Mirjam Schöttle, Jakob Ullrich, Roland T Altmüller, Janine Becker, Christian Nürnberg, Peter Seidel, Henrik Böhm, Diana Göke, Friederike Ansén, Sascha Russell, Prudence A Wright, Gavin M Wainer, Zoe Solomon, Benjamin Petersen, Iver Clement, Joachim H Sänger, Jörg Brustugun, Odd-Terje Helland, Åslaug Solberg, Steinar Lund-Iversen, Marius Buettner, Reinhard Wolf, Jürgen Brambilla, Elisabeth Vingron, Martin Perner, Sven Haas, Stefan A Thomas, Roman K |
| description | 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. |
| doi_str_mv | 10.1186/s13059-014-0558-0 |
| format | Article |
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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.</description><identifier>ISSN: 1465-6906</identifier><identifier>ISSN: 1474-7596</identifier><identifier>EISSN: 1474-760X</identifier><identifier>EISSN: 1465-6906</identifier><identifier>EISSN: 1465-6914</identifier><identifier>DOI: 10.1186/s13059-014-0558-0</identifier><identifier>PMID: 25650807</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Algorithms ; Analysis ; Base Sequence ; Bioinformatics ; Cancer ; Candidates ; carcinogenesis ; Care and treatment ; Cell Line, Tumor ; Chromosome Breakpoints ; Cluster Analysis ; Computational Biology - methods ; Computer applications ; Diagnosis ; Gene expression ; Gene Silencing ; Genes ; Genetic aspects ; Genetic research ; Genomes ; Genomics ; Health aspects ; High-Throughput Nucleotide Sequencing ; Humans ; Identification ; In Situ Hybridization, Fluorescence ; Kinases ; Lung cancer ; lung neoplasms ; Lung Neoplasms - genetics ; lungs ; Method ; Mutation ; Oncogene Fusion ; Oncogene Proteins, Fusion - genetics ; Performance evaluation ; Pipelines ; Proteins ; Ribonucleic acid ; RNA ; sequence analysis ; Therapeutic applications ; therapeutics ; Transcriptome ; Translocation, Genetic ; Tumor Suppressor Proteins - genetics ; Tumors</subject><ispartof>Genome Biology, 2015-01, Vol.16 (1), p.7-7, Article 7</ispartof><rights>COPYRIGHT 2015 BioMed Central Ltd.</rights><rights>2015. This work is licensed under http://creativecommons.org/licenses/by/4.0 (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Fernandez-Cuesta et al.; licensee BioMed Central. 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c628t-242444bc8a2d02a4793402c6e8281088d8b070befed9efdfe50f0e3f3433a3243</citedby><cites>FETCH-LOGICAL-c628t-242444bc8a2d02a4793402c6e8281088d8b070befed9efdfe50f0e3f3433a3243</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300615/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300615/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25650807$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fernandez-Cuesta, Lynnette</creatorcontrib><creatorcontrib>Sun, Ruping</creatorcontrib><creatorcontrib>Menon, Roopika</creatorcontrib><creatorcontrib>George, Julie</creatorcontrib><creatorcontrib>Lorenz, Susanne</creatorcontrib><creatorcontrib>Meza-Zepeda, Leonardo A</creatorcontrib><creatorcontrib>Peifer, Martin</creatorcontrib><creatorcontrib>Plenker, Dennis</creatorcontrib><creatorcontrib>Heuckmann, Johannes M</creatorcontrib><creatorcontrib>Leenders, Frauke</creatorcontrib><creatorcontrib>Zander, Thomas</creatorcontrib><creatorcontrib>Dahmen, Ilona</creatorcontrib><creatorcontrib>Koker, Mirjam</creatorcontrib><creatorcontrib>Schöttle, Jakob</creatorcontrib><creatorcontrib>Ullrich, Roland T</creatorcontrib><creatorcontrib>Altmüller, Janine</creatorcontrib><creatorcontrib>Becker, Christian</creatorcontrib><creatorcontrib>Nürnberg, Peter</creatorcontrib><creatorcontrib>Seidel, Henrik</creatorcontrib><creatorcontrib>Böhm, Diana</creatorcontrib><creatorcontrib>Göke, Friederike</creatorcontrib><creatorcontrib>Ansén, Sascha</creatorcontrib><creatorcontrib>Russell, Prudence A</creatorcontrib><creatorcontrib>Wright, Gavin M</creatorcontrib><creatorcontrib>Wainer, Zoe</creatorcontrib><creatorcontrib>Solomon, Benjamin</creatorcontrib><creatorcontrib>Petersen, Iver</creatorcontrib><creatorcontrib>Clement, Joachim H</creatorcontrib><creatorcontrib>Sänger, Jörg</creatorcontrib><creatorcontrib>Brustugun, Odd-Terje</creatorcontrib><creatorcontrib>Helland, Åslaug</creatorcontrib><creatorcontrib>Solberg, Steinar</creatorcontrib><creatorcontrib>Lund-Iversen, Marius</creatorcontrib><creatorcontrib>Buettner, Reinhard</creatorcontrib><creatorcontrib>Wolf, Jürgen</creatorcontrib><creatorcontrib>Brambilla, Elisabeth</creatorcontrib><creatorcontrib>Vingron, Martin</creatorcontrib><creatorcontrib>Perner, Sven</creatorcontrib><creatorcontrib>Haas, Stefan A</creatorcontrib><creatorcontrib>Thomas, Roman K</creatorcontrib><title>Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data</title><title>Genome Biology</title><addtitle>Genome Biol</addtitle><description>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.</description><subject>Algorithms</subject><subject>Analysis</subject><subject>Base Sequence</subject><subject>Bioinformatics</subject><subject>Cancer</subject><subject>Candidates</subject><subject>carcinogenesis</subject><subject>Care and treatment</subject><subject>Cell Line, Tumor</subject><subject>Chromosome Breakpoints</subject><subject>Cluster Analysis</subject><subject>Computational Biology - methods</subject><subject>Computer applications</subject><subject>Diagnosis</subject><subject>Gene expression</subject><subject>Gene Silencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic research</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Health aspects</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humans</subject><subject>Identification</subject><subject>In Situ Hybridization, Fluorescence</subject><subject>Kinases</subject><subject>Lung cancer</subject><subject>lung neoplasms</subject><subject>Lung Neoplasms - genetics</subject><subject>lungs</subject><subject>Method</subject><subject>Mutation</subject><subject>Oncogene Fusion</subject><subject>Oncogene Proteins, Fusion - genetics</subject><subject>Performance evaluation</subject><subject>Pipelines</subject><subject>Proteins</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>sequence analysis</subject><subject>Therapeutic applications</subject><subject>therapeutics</subject><subject>Transcriptome</subject><subject>Translocation, Genetic</subject><subject>Tumor Suppressor Proteins - genetics</subject><subject>Tumors</subject><issn>1465-6906</issn><issn>1474-7596</issn><issn>1474-760X</issn><issn>1465-6906</issn><issn>1465-6914</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>KPI</sourceid><sourceid>BENPR</sourceid><recordid>eNqFkktv1DAUhSMEomXgB7BBkdiURcr1M84Gqap4jKgEC5DYWY5zPbgk9mAnFf33OJpSMWyQF_a1v3Ple3Sq6jmBc0KUfJ0JA9E1QHgDQqgGHlSnhLe8aSV8e7iepWhkB_KkepLzNQDpOJWPqxMqpAAF7WkVtgOG2TtvzexjqKOrQ7zBsXZLXusdBsy1D_W4hF1tTbCY6vJUij6h-bGPPsy1yRmnfrxd5XMyIdvk93OcsM74c8FgV34ws3laPXJmzPjsbt9UX9-9_XL5obn69H57eXHVWEnV3FBOOee9VYYOQA1vO8aBWomKKgJKDaqHFnp0OHToBocCHCBzjDNmGOVsU7059N0v_YSDLTMmM-p98pNJtzoar49fgv-ud_FGcwYgiSgNzu4apFgmyLOefLY4jiZgXLKmAMC4aLv_o0RK4IRxtaIv_0Gv45JCcUJTCq1gQnS0UOcHamdG1D64WL5oyxpw8jYGdL7cXwhOCq2KN5vq1ZGgMDP-mndmyVl__Lw9ZsmBtSnmnNDdm0JAr6nSh1Tpkiq9pkpD0bz42817xZ8Ysd_df8hv</recordid><startdate>20150105</startdate><enddate>20150105</enddate><creator>Fernandez-Cuesta, 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of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data</title><author>Fernandez-Cuesta, Lynnette ; Sun, Ruping ; Menon, Roopika ; George, Julie ; Lorenz, Susanne ; Meza-Zepeda, Leonardo A ; Peifer, Martin ; Plenker, Dennis ; Heuckmann, Johannes M ; Leenders, Frauke ; Zander, Thomas ; Dahmen, Ilona ; Koker, Mirjam ; Schöttle, Jakob ; Ullrich, Roland T ; Altmüller, Janine ; Becker, Christian ; Nürnberg, Peter ; Seidel, Henrik ; Böhm, Diana ; Göke, Friederike ; Ansén, Sascha ; Russell, Prudence A ; Wright, Gavin M ; Wainer, Zoe ; Solomon, Benjamin ; Petersen, Iver ; Clement, Joachim H ; Sänger, Jörg ; Brustugun, Odd-Terje ; Helland, Åslaug ; Solberg, Steinar ; Lund-Iversen, Marius ; Buettner, Reinhard ; Wolf, Jürgen ; Brambilla, Elisabeth ; Vingron, Martin ; Perner, Sven ; Haas, Stefan A ; Thomas, Roman 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Central China</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genome Biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fernandez-Cuesta, Lynnette</au><au>Sun, Ruping</au><au>Menon, Roopika</au><au>George, Julie</au><au>Lorenz, Susanne</au><au>Meza-Zepeda, Leonardo A</au><au>Peifer, Martin</au><au>Plenker, Dennis</au><au>Heuckmann, Johannes M</au><au>Leenders, Frauke</au><au>Zander, Thomas</au><au>Dahmen, Ilona</au><au>Koker, Mirjam</au><au>Schöttle, Jakob</au><au>Ullrich, Roland T</au><au>Altmüller, Janine</au><au>Becker, Christian</au><au>Nürnberg, Peter</au><au>Seidel, Henrik</au><au>Böhm, Diana</au><au>Göke, Friederike</au><au>Ansén, Sascha</au><au>Russell, Prudence A</au><au>Wright, Gavin M</au><au>Wainer, Zoe</au><au>Solomon, Benjamin</au><au>Petersen, Iver</au><au>Clement, Joachim H</au><au>Sänger, Jörg</au><au>Brustugun, Odd-Terje</au><au>Helland, Åslaug</au><au>Solberg, Steinar</au><au>Lund-Iversen, Marius</au><au>Buettner, Reinhard</au><au>Wolf, Jürgen</au><au>Brambilla, Elisabeth</au><au>Vingron, Martin</au><au>Perner, Sven</au><au>Haas, Stefan A</au><au>Thomas, Roman K</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data</atitle><jtitle>Genome Biology</jtitle><addtitle>Genome Biol</addtitle><date>2015-01-05</date><risdate>2015</risdate><volume>16</volume><issue>1</issue><spage>7</spage><epage>7</epage><pages>7-7</pages><artnum>7</artnum><issn>1465-6906</issn><issn>1474-7596</issn><eissn>1474-760X</eissn><eissn>1465-6906</eissn><eissn>1465-6914</eissn><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.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>25650807</pmid><doi>10.1186/s13059-014-0558-0</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1465-6906 |
| ispartof | Genome Biology, 2015-01, Vol.16 (1), p.7-7, Article 7 |
| issn | 1465-6906 1474-7596 1474-760X 1465-6906 1465-6914 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4300615 |
| source | MEDLINE; Springer Nature - Complete Springer Journals; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Springer Nature OA Free Journals |
| subjects | Algorithms Analysis Base Sequence Bioinformatics Cancer Candidates carcinogenesis Care and treatment Cell Line, Tumor Chromosome Breakpoints Cluster Analysis Computational Biology - methods Computer applications Diagnosis Gene expression Gene Silencing Genes Genetic aspects Genetic research Genomes Genomics Health aspects High-Throughput Nucleotide Sequencing Humans Identification In Situ Hybridization, Fluorescence Kinases Lung cancer lung neoplasms Lung Neoplasms - genetics lungs Method Mutation Oncogene Fusion Oncogene Proteins, Fusion - genetics Performance evaluation Pipelines Proteins Ribonucleic acid RNA sequence analysis Therapeutic applications therapeutics Transcriptome Translocation, Genetic Tumor Suppressor Proteins - genetics Tumors |
| title | Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data |
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