Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data
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- 作者：Lynnette Fernandez-Cuesta (1) (2)
Ruping Sun (3) (4)
Roopika Menon (5) (6)
Julie George (1)
Susanne Lorenz (7)
Leonardo A Meza-Zepeda (7)
Martin Peifer (1) (8)
Dennis Plenker (1)
Johannes M Heuckmann (6)
Frauke Leenders (1)
Thomas Zander (1) (10) (9)
Ilona Dahmen (1)
Mirjam Koker (1)
Jakob Sch枚ttle (1) (11)
Roland T Ullrich (11) (8) (9)
Janine Altm眉ller (12) (13) (14)
Christian Becker (12)
Peter N眉rnberg (12) (13)
Henrik Seidel (15)
Diana B枚hm (5)
Friederike G枚ke (5)
Sascha Ans茅n (9)
Prudence A Russell (16)
Gavin M Wright (17)
Zoe Wainer (17)
Benjamin Solomon (18)
Iver Petersen (19)
Joachim H Clement (20)
J枚rg S盲nger (21)
Odd-Terje Brustugun (22) (23)
脜slaug Helland (22) (23)
Steinar Solberg (24)
Marius Lund-Iversen (25)
Reinhard Buettner (10) (26)
J眉rgen Wolf (10) (9)
Elisabeth Brambilla (27)
Martin Vingron (3)
Sven Perner (5)
Stefan A Haas (3)
Roman K Thomas (1) (26) - 刊名：Genome Biology
- 出版年：2015
- 出版时间：December 2015
- 年：2015
- 卷：16
- 期：1
- 全文大小：1,888 KB
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Ruping Sun (3) (4)
Roopika Menon (5) (6)
Julie George (1)
Susanne Lorenz (7)
Leonardo A Meza-Zepeda (7)
Martin Peifer (1) (8)
Dennis Plenker (1)
Johannes M Heuckmann (6)
Frauke Leenders (1)
Thomas Zander (1) (10) (9)
Ilona Dahmen (1)
Mirjam Koker (1)
Jakob Sch枚ttle (1) (11)
Roland T Ullrich (11) (8) (9)
Janine Altm眉ller (12) (13) (14)
Christian Becker (12)
Peter N眉rnberg (12) (13)
Henrik Seidel (15)
Diana B枚hm (5)
Friederike G枚ke (5)
Sascha Ans茅n (9)
Prudence A Russell (16)
Gavin M Wright (17)
Zoe Wainer (17)
Benjamin Solomon (18)
Iver Petersen (19)
Joachim H Clement (20)
J枚rg S盲nger (21)
Odd-Terje Brustugun (22) (23)
脜slaug Helland (22) (23)
Steinar Solberg (24)
Marius Lund-Iversen (25)
Reinhard Buettner (10) (26)
J眉rgen Wolf (10) (9)
Elisabeth Brambilla (27)
Martin Vingron (3)
Sven Perner (5)
Stefan A Haas (3)
Roman K Thomas (1) (26)
1. Department of Translational Genomics, Center of Integrated Oncology Cologne鈥揃onn, Medical Faculty, University of Cologne, 50924, Cologne, Germany
2. Genetic Cancer Susceptibility Group, Section of Genetics, International Agency for Research on Cancer (IARC-WHO), 69008, Lyons, France
3. Computational Molecular Biology Group, Max Planck Institute for Molecular Genetics, D-14195, Berlin, Germany
4. Department of Systems Biology, Columbia University, New York, NY, 10032, USA
5. Department of Prostate Cancer Research, Institute of Pathology, Center for Integrated Oncology Cologne-Bonn, University Hospital of Bonn, Bonn, Germany
6. Blackfield AG, Gottfried-Hagen-Str. 60, 51105, Cologne, Germany
7. Department of Tumor Biology and Genomics Core Facility, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway
8. Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
10. Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne-Bonn, 50924, Cologne, Germany
9. Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University of Cologne, 50924, Cologne, Germany
11. Max Planck Institute for Neurological Research, 50931, Cologne, Germany
12. Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931, Germany
13. Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
14. Institute of Human Genetics, University of Cologne, 50931, Cologne, Germany
15. Bayer Schering, Berlin, Germany
16. Department of Pathology, St. Vincent鈥檚 Hospital, Melbourne, 3065, Victoria, Australia
17. University of Melbourne Department of Surgery, St Vincent鈥檚 Hospital, Melbourne, 3065, Victoria, Australia
18. Department of Haematology and Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, 3002, Victoria, Australia
19. Institute of Pathology, Jena University Hospital, Friedrich-Schiller-University, 07743, Jena, Germany
20. Department of Internal Medicine II, Jena University Hospital, Friedrich-Schiller-University, 07743, Jena, Germany
21. Institute for Pathology Bad Berka, 99438, Bad Berka, Germany
22. Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0424, Oslo, Norway
23. Department of Oncology, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway
24. Department of Thoracic Surgery, Rikshospitalet, Oslo University Hospital, N-0027, Oslo, Norway
25. Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway
26. Department of Pathology, University Hospital Medical Center, University of Cologne, 50937, Cologne, Germany
27. Department of Pathology, CHU Grenoble INSERM U823, Institute Albert Bonniot, 38043 CS10217, Grenoble, France - 刊物主题：Animal Genetics and Genomics; Human Genetics; Plant Genetics & Genomics; Microbial Genetics and Genomics; Fungus Genetics; Bioinformatics;
- 出版者：BioMed Central
- ISSN：1465-6906
文摘
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.