ArticleBioinformatics (Oxford, England)2011
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 57 citations in OpenAlex.
- A multi-tissue, splicing-based joint transcriptome-wide association study identifies susceptibility genes for breast cancer.American journal of human genetics · 2024Article
- LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.BMC genomics · 2020Article
- Detection of novel fusion-transcripts by RNA-Seq in T-cell lymphoblastic lymphoma.Scientific reports · 2019Article
- A fast detection of fusion genes from paired-end RNA-seq data.BMC genomics · 2018Article
- Identification ofOncotarget · 2017Article
- Statistical algorithms improve accuracy of gene fusion detection.Nucleic acids research · 2017Article
- Article
- Identifying fusion transcripts using next generation sequencing.Wiley interdisciplinary reviews. RNA · 2016Review
- Discovering and understanding oncogenic gene fusions through data intensive computational approaches.Nucleic acids research · 2016Review
- Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data.Nucleic acids research · 2016Article
- Detecting and targetting oncogenic fusion proteins in the genomic era.Biology of the cell · 2015Review
- FANSe2: a robust and cost-efficient alignment tool for quantitative next-generation sequencing applications.PloS one · 2014Article
- Article
- Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.PloS one · 2014Article
- TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads.BMC genomics · 2014Article
- Fusion genes and their discovery using high throughput sequencing.Cancer letters · 2013Review
- Next-generation sequencing in the clinic: promises and challenges.Cancer letters · 2013Review
- Identification of cancer gene fusions based on advanced analysis of the human genome or transcriptome.Frontiers of medicine · 2013Review
- Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives.Briefings in bioinformatics · 2013Review
- Existing and emerging technologies for tumor genomic profiling.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2013Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
motivationPaired-end whole transcriptome sequencing provides evidence for fusion transcripts. However, due to the repetitiveness of the transcriptome, many reads have multiple high-quality mappings. Previous methods to find gene fusions either ignored these reads or required additional longer single reads. This can obscure up to 30% of fusions and unnecessarily discards much of the data.
resultsWe present a method for using paired-end reads to find fusion transcripts without requiring unique mappings or additional single read sequencing. Using simulated data and data from tumors and cell lines, we show that our method can find fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations. AVAILABILITY: A C++ and Python implementation of the method demonstrated in this article is available at http://exon.ucsd.edu/ShortFuse. CONTACT: mckinsel@ucsd.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.