ArticleBMC genomics2019
Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 2 of them syntheses that pooled it.
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
56 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Non-coding RNA profiles associated with equine osteoarthritis: a systematic review.Frontiers in veterinary science · 2026Pooled it
- A systematic review of non-coding RNA genes with differential expression profiles associated with autism spectrum disorders.PloS one · 2023Pooled it
- A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker).RNA (New York, N.Y.) · 2026Article
- Cellular-state control using ribozyme-scaffolded miRNA-sensing and CRISPR-mediated actuation.Cell reports methods · 2026Article
- Micro RNA Sequencing in Circulating Tumor Cells.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Optimizing Small RNA Sequencing for Salivary Biomarker Identification: A Comparative Study of Library Preparation Protocols.International journal of molecular sciences · 2025Article
- MicroRNA expression in peripheral blood of children with asthma and the role of miR-31-5p in childhood asthma progression.Scientific reports · 2025Article
- Expression Profiles of Exosomal miRNAs in Gaucher Patients and Their Association With Severity of Bone Involvement.Journal of inherited metabolic disease · 2025Article
- Evaluating Genetic Regulators of MicroRNAs Using Machine Learning Models.International journal of molecular sciences · 2025Article
- miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs.Genome biology · 2025Article
- Beyond the Bubble: A Debate on microRNA Sorting Into Extracellular Vesicles.Laboratory investigation; a journal of technical methods and pathology · 2025Review
- Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing.Cell reports methods · 2024Article
- Characteristics of MicroRNA Expression Depending on the Presence or Absence of Meningioma in Patients with Neurofibromatosis Type 2: A Secondary Analysis.Neurologia medico-chirurgica · 2024Article
- Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases.Molecular therapy. Nucleic acids · 2024Review
- Mesenchymal stromal cell derived extracellular vesicles as a therapeutic tool: immune regulation, MSC priming, and applications to SLE.Frontiers in immunology · 2024Review
- Single Cell Micro RNA Sequencing Library Preparation.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The Typical tRNA Co-Expresses Multiple 5' tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease.Non-coding RNA · 2023Article
- Urinary phthalate metabolites and small non-coding RNAs from seminal plasma extracellular vesicles among men undergoing infertility treatment.Environmental pollution (Barking, Essex : 1987) · 2023Article
- Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling.Plant molecular biology · 2023Article
- Epigenetic Mechanisms and Nephrotic Syndrome: A Systematic Review.Biomedicines · 2023Review
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapter ligation bias with limited evaluation of reverse transcription bias or amplification bias. Furthermore, evaluations of the quantification of isomiRs (miRNA isoforms) or the influence of starting amount on performance have been very limited. No study had yet evaluated the quantification of isomiRs of altered length or compared the consistency of results derived from multiple moderate starting inputs. We therefore evaluated quantifications of miRNA and isomiRs using four library preparation kits, with various starting amounts, as well as quantifications following removal of duplicate reads using unique molecular identifiers (UMIs) to mitigate reverse transcription and amplification biases.
resultsAll methods resulted in false isomiR detection; however, the adapter-free method tested was especially prone to false isomiR detection. We demonstrate that using UMIs improves accuracy and we provide a guide for input amounts to improve consistency.
conclusionsOur data show differences and limitations of current methods, thus raising concerns about the validity of quantification of miRNA and isomiRs across studies. We advocate for the use of UMIs to improve accuracy and reliability of miRNA quantifications.
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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.