title: Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.
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.
authors: Lynnette
authors: L
authors: Fernandez-Cuesta
authors: Ruping
authors: R
authors: Sun
authors: Roopika
authors: R
authors: Menon
authors: Julie
authors: J
authors: George
authors: Susanne
authors: S
authors: Lorenz
authors: Leonardo A
authors: LA
authors: Meza-Zepeda
authors: Martin
authors: M
authors: Peifer
authors: Dennis
authors: D
authors: Plenker
authors: Johannes M
authors: JM
authors: Heuckmann
authors: Frauke
authors: F
authors: Leenders
authors: Thomas
authors: T
authors: Zander
authors: Ilona
authors: I
authors: Dahmen
authors: Mirjam
authors: M
authors: Koker
authors: Jakob
authors: J
authors: Schöttle
authors: Roland T
authors: RT
authors: Ullrich
authors: Janine
authors: J
authors: Altmüller
authors: Christian
authors: C
authors: Becker
authors: Peter
authors: P
authors: Nürnberg
authors: Henrik
authors: H
authors: Seidel
authors: Diana
authors: D
authors: Böhm
authors: Friederike
authors: F
authors: Göke
authors: Sascha
authors: S
authors: Ansén
authors: Prudence A
authors: PA
authors: Russell
authors: Gavin M
authors: GM
authors: Wright
authors: Zoe
authors: Z
authors: Wainer
authors: Benjamin
authors: B
authors: Solomon
authors: Iver
authors: I
authors: Petersen
authors: Joachim H
authors: JH
authors: Clement
authors: Jörg
authors: J
authors: Sänger
authors: Odd-Terje
authors: OT
authors: Brustugun
authors: Åslaug
authors: Å
authors: Helland
authors: Steinar
authors: S
authors: Solberg
authors: Marius
authors: M
authors: Lund-Iversen
authors: Reinhard
authors: R
authors: Buettner
authors: Jürgen
authors: J
authors: Wolf
authors: Elisabeth
authors: E
authors: Brambilla
authors: Martin
authors: M
authors: Vingron
authors: Sven
authors: S
authors: Perner
authors: Stefan A
authors: SA
authors: Haas
authors: Roman K
authors: RK
authors: Thomas
mesh_terms: D001483:Base Sequence; D045744:Cell Line, Tumor; D056905:Chromosome Breakpoints; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D020868:Gene Silencing; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008175:Lung Neoplasms / Q000235:genetics; D050596:Oncogene Fusion; D015514:Oncogene Proteins, Fusion / Q000235:genetics; D059467:Transcriptome; D014178:Translocation, Genetic; D025521:Tumor Suppressor Proteins / Q000235:genetics
chemical_list: C522504:EML4-ALK fusion protein, human; D015514:Oncogene Proteins, Fusion; C512680:RASSF8 protein, human; D025521:Tumor Suppressor Proteins
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