ArticleBMC genomics2016
Impact of RNA degradation on fusion detection by RNA-seq.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- A prospective clinical and biological database for pancreatic adenocarcinoma: the BACAP cohort.BMC cancer · 2018Trial
- Detection of Fusion Genes Using RNA Sequencing in Acute Leukemia.Annals of laboratory medicine · 2026Article
- PACLseq: A Standalone Diagnostic Method for Ph-Like Acute Lymphoblastic Leukemia Using Nanopore Sequencing.MedComm · 2025Article
- Article
- A comprehensive assessment of exome capture methods for RNA sequencing of formalin-fixed and paraffin-embedded samples.BMC genomics · 2023Review
- Molecular diagnostic tools for the World Health Organization (WHO) 2021 classification of gliomas, glioneuronal and neuronal tumors; an EANO guideline.Neuro-oncology · 2023Article
- Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing.Nature communications · 2022Article
- A novel WWTR1::AFF2 fusion in an intra-abdominal soft tissue sarcoma with associated endometriosis.Genes, chromosomes & cancer · 2022Article
- Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation.Journal of clinical and translational hepatology · 2022Review
- SCISSOR: a framework for identifying structural changes in RNA transcripts.Nature communications · 2021Article
- RNAseq Analysis of Rodent Spaceflight Experiments Is Confounded by Sample Collection Techniques.iScience · 2020Article
- Low RIN Value for RNA-Seq Library Construction from Long-Term Stored Seeds: A Case Study of Barley Seeds.Genes · 2020Article
- Xanthogranulomatous epithelial tumor: report of 6 cases of a novel, potentially deceptive lesion with a predilection for young women.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2020Article
- Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle.BMC genomics · 2020Article
- Reference-free transcriptome exploration reveals novel RNAs for prostate cancer diagnosis.Life science alliance · 2019Article
- Leiomyoma with KAT6B-KANSL1 fusion: case report of a rapidly enlarging uterine mass in a postmenopausal woman.Diagnostic pathology · 2019Article
- RNA sequencing and swarm intelligence-enhanced classification algorithm development for blood-based disease diagnostics using spliced blood platelet RNA.Nature protocols · 2019Article
- Genetic insights into the neurodevelopmental origins of schizophrenia.Nature reviews. Neuroscience · 2017Review
- Gastroblastoma harbors a recurrent somatic MALAT1-GLI1 fusion gene.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2017Article
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA-seq is a well-established method for studying the transcriptome. Popular methods for library preparation in RNA-seq such as Illumina TruSeq® RNA v2 kit use a poly-A pulldown strategy. Such methods can cause loss of coverage at the 5' end of genes, impacting the ability to detect fusions when used on degraded samples. The goal of this study was to quantify the effects RNA degradation has on fusion detection when using poly-A selected mRNA and to identify the variables involved in this process.
resultsUsing both artificially and naturally degraded samples, we found that there is a reduced ability to detect fusions as the distance of the breakpoint from the 3' end of the gene increases. The median transcript coverage decreases exponentially as a function of the distance from the 3' end and there is a linear relationship between the coverage decay rate and the RNA integrity number (RIN). Based on these findings we developed plots that show the probability of detecting a gene fusion ("sensitivity") as a function of the distance of the fusion breakpoint from the 3' end.
conclusionsThis study developed a strategy to assess the impact that RNA degradation has on the ability to detect gene fusions by RNA-seq.
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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.