ArticleGenome biology2015
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed, 51 citations in OpenAlex.
- Article
- Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer.The Journal of clinical investigation · 2023Article
- RNA-seq data science: From raw data to effective interpretation.Frontiers in genetics · 2023Review
- Molecular Pathology of Lung Cancer.Cold Spring Harbor perspectives in medicine · 2022Review
- Identification and Characterization of Non-Coding RNAs in Thymoma.Medical science monitor : international medical journal of experimental and clinical research · 2021Article
- Ferroptosis response segregates small cell lung cancer (SCLC) neuroendocrine subtypes.Nature communications · 2021Article
- CRTC1/MAML2 directs a PGC-1α-IGF-1 circuit that confers vulnerability to PPARγ inhibition.Cell reports · 2021Article
- Application of Next Generation Sequencing in Laboratory Medicine.Annals of laboratory medicine · 2021Review
- Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids.Nature communications · 2019Article
- Discovery of New Fusion Transcripts in a Cohort of Pediatric Solid Cancers at Relapse and Relevance for Personalized Medicine.Molecular therapy : the journal of the American Society of Gene Therapy · 2019Article
- A fast detection of fusion genes from paired-end RNA-seq data.BMC genomics · 2018Article
- TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data.BMC medical genomics · 2018Article
- Article
- Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors.Nature communications · 2018Article
- Targeting a non-oncogene addiction to the ATR/CHK1 axis for the treatment of small cell lung cancer.Scientific reports · 2017Article
- LSD1 modulates the non-canonical integrin β3 signaling pathway in non-small cell lung carcinoma cells.Scientific reports · 2017Article
- Statistical algorithms improve accuracy of gene fusion detection.Nucleic acids research · 2017Article
- Multiplexed transcriptome analysis to detect ALK, ROS1 and RET rearrangements in lung cancer.Scientific reports · 2017Article
- A novel read-through transcript JMJD7-PLA2G4B regulates head and neck squamous cell carcinoma cell proliferation and survival.Oncotarget · 2017Article
- ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.BMC genomics · 2017Article
Corrections and comments
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Authors and funding
40 authors at 17 institutions in 6 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.