ArticlePloS one2015
An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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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
28 citing papers in PubMed, 65 citations in OpenAlex.
- Real-time and programmable transcriptome sequencing with PROFIT-seq.Nature cell biology · 2024Article
- Sarcomas with EWSR1::Non-ETS Fusion (EWSR1::NFATC2 and EWSR1::PATZ1).Surgical pathology clinics · 2024Review
- Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep (PeerJ · 2024Article
- An optimized workflow of full-length transcriptome sequencing for accurate fusion transcript identification.RNA biology · 2024Article
- The Efficacy of Molecular Analysis in the Diagnosis of Bone and Soft Tissue Sarcoma: A 15-Year Mono-Institutional Study.International journal of molecular sciences · 2022Article
- Advances and Trends in Omics Technology Development.Frontiers in medicine · 2022Review
- Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs.Conservation genetics resources · 2022Article
- K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology.Plant methods · 2021Article
- An All-In-One Transcriptome-Based Assay to Identify Therapy-Guiding Genomic Aberrations in Nonsmall Cell Lung Cancer Patients.Cancers · 2020Article
- RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens.Biomedicines · 2020Article
- RNA-Based Detection of Gene Fusions in Formalin-Fixed and Paraffin-Embedded Solid Cancer Samples.Cancers · 2019Article
- New fusion sarcomas: histopathology and clinical significance of selected entities.Human pathology · 2019Review
- Targeted Single Primer Enrichment Sequencing with Single End Duplex-UMI.Scientific reports · 2019Article
- Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier.BMC genomics · 2019Article
- BRAF fusions identified in melanomas have variable treatment responses and phenotypes.Oncogene · 2019Article
- Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA.PloS one · 2019Article
- Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm.Frontiers in plant science · 2019Article
- ALK Inhibitor Response in Melanomas ExpressingMolecular cancer therapeutics · 2018Article
- Optimization of RNA Extraction from Formalin-Fixed Paraffin-Embedded Blocks for Targeted Next-Generation Sequencing.Journal of breast cancer · 2017Article
- Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors.The Journal of molecular diagnostics : JMD · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fusion genes are known to be key drivers of tumor growth in several types of cancer. Traditionally, detecting fusion genes has been a difficult task based on fluorescent in situ hybridization to detect chromosomal abnormalities. More recently, RNA sequencing has enabled an increased pace of fusion gene identification. However, RNA-Seq is inefficient for the identification of fusion genes due to the high number of sequencing reads needed to detect the small number of fusion transcripts present in cells of interest. Here we describe a method, Single Primer Enrichment Technology (SPET), for targeted RNA sequencing that is customizable to any target genes, is simple to use, and efficiently detects gene fusions. Using SPET to target 5701 exons of 401 known cancer fusion genes for sequencing, we were able to identify known and previously unreported gene fusions from both fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue RNA in both normal tissue and cancer cells.
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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.