ReviewJournal of Cancer2015
Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers.
Review in Journal of Cancer, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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.
The trial behind it
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
25 citing papers in PubMed, 38 citations in OpenAlex.
- The hidden sources of spurious fusion transcripts in plants.Genome biology · 2026Article
- FuSViz-visualization and interpretation of structural variation using cancer genomics and transcriptomics data.Nucleic acids research · 2025Article
- Technology to the rescue: how to uncover the role of transposable elements in preimplantation development.Biochemical Society transactions · 2024Review
- Anchored-fusion enables targeted fusion search in bulk and single-cell RNA sequencing data.Cell reports methods · 2024Article
- TargetedCell reports methods · 2023Article
- Establishment of New Genetic Markers and Methods for Sex Determination of Mouse and Human Cells using Polymerase Chain Reactions and Crude DNA Samples.Current genomics · 2022Article
- Reply to Grigoriev et al., "Sequences of SARS-CoV-2 'Hybrids' with the Human Genome: Signs of Non-coding RNA?"Journal of virology · 2022Article
- RNA expression profiling from the liquid fraction of synovial fluid in knee joint osteoarthritis patients.American journal of translational research · 2022Article
- Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology.NPJ precision oncology · 2021Review
- SARS-CoV-2-Host Chimeric RNA-Sequencing Reads Do Not Necessarily Arise From Virus Integration Into the Host DNA.Frontiers in microbiology · 2021Article
- Evidence of constraint in the 3D genome for trans-splicing in human cells.Science China. Life sciences · 2020Article
- Computational Detection of Known Pathogenic Gene Fusions in a Normal Tissue Database and Implications for Genetic Disease Research.Frontiers in genetics · 2020Article
- A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease.PloS one · 2019Article
- Circular RNA Profiling by Illumina Sequencing via Template-Dependent Multiple Displacement Amplification.BioMed research international · 2019Article
- Expanding primary cells from mucoepidermoid and other salivary gland neoplasms for genetic and chemosensitivity testing.Disease models & mechanisms · 2018Article
- Review
- While it is not deliberate, much of today's biomedical research contains logical and technical flaws, showing a need for corrective action.International journal of medical sciences · 2018Review
- Article
- It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research.International journal of molecular sciences · 2017Review
- New chimeric RNAs in acute myeloid leukemia.F1000Research · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent RNA-sequencing technology and associated bioinformatics have led to identification of tens of thousands of putative human chimeric RNAs, i.e. RNAs containing sequences from two different genes, most of which are derived from neighboring genes on the same chromosome. In this essay, we redefine "two neighboring genes" as those producing individual transcripts, and point out two known mechanisms for chimeric RNA formation, i.e. transcription from a fusion gene or trans-splicing of two RNAs. By our definition, most putative RNA chimeras derived from canonically-defined neighboring genes may either be technical artifacts or be cis-splicing products of 5'- or 3'-extended RNA of either partner that is redefined herein as an unannotated gene, whereas trans-splicing events are rare in human cells. Therefore, most authentic chimeric RNAs result from fusion genes, about 1,000 of which have been identified hitherto. We propose a hypothesis of "consecutive reverse transcriptions (RTs)", i.e. another RT reaction following the previous one, for how most spurious chimeric RNAs, especially those containing a short homologous sequence, may be generated during RT, especially in RNA-sequencing wherein RNAs are fragmented. We also point out that RNA samples contain numerous RNA and DNA shreds that can serve as endogenous random primers for RT and ensuing polymerase chain reactions (PCR), creating artifacts in RT-PCR.
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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.