ArticleGenome biology2022
Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 29 citations in OpenAlex.
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- HiFi long-read RNA sequencing enhances clinical diagnostics in rare disorders.European journal of human genetics : EJHG · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- An rRNA-depleted full-length transcriptome strategy using nanopore sequencing for identification of novel lncRNA isoforms.Communications biology · 2026Article
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- Alternative splicing in pediatric central nervous system tumors highlights oncofetal candidateNeuro-oncology pediatrics · 2026Article
- Isoformic: a workflow for transcript-level RNA-seq interpretation.NAR genomics and bioinformatics · 2025Article
- Full-length hybrid transcriptome of the olfactory rosette in Senegalese sole (Solea senegalensis): an essential genomic resource for improving reproduction on farms.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Protein arginine methyltransferase 5 sustains Tip60-EP400 complex via SRSF1 in Merkel cell carcinoma.Life science alliance · 2025Article
- RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks.Bioinformatics (Oxford, England) · 2025Article
- Alternative splicing fine-tunes prey shift of Coccinellini lady beetles to non-target insect.BMC genomics · 2025Article
- Profiling genetically driven alternative splicing across the Indonesian archipelago.American journal of human genetics · 2024Article
- Article
- Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity.BMC genomics · 2024Article
- RNA in axons, dendrites, synapses and beyond.Frontiers in molecular neuroscience · 2024Review
- A proteogenomic atlas of the human neural retina.Frontiers in genetics · 2024Article
- Single-cell long-read sequencing in human cerebral organoids uncovers cell-type-specific and autism-associated exons.Cell reports · 2023Article
- Comprehensive analysis of alternative splicing across multiple transcriptomic cohorts reveals prognostic signatures in prostate cancer.Human genomics · 2023Article
- Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis.Briefings in bioinformatics · 2023Review
- Long-Read Sequencing in Blood Group Genetics.Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie · 2023Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThere is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by overlapping genes and transcripts as well as the presence of unprocessed or partially processed RNAs.
resultsWe compared introns detected by 8 tools using short RNA-seq reads with introns observed in long RNA-seq reads from the same biological specimens. We found significant disagreement among tools (Fleiss' [Formula: see text]) such that 47.7% of all detected intron retentions were not called by more than one tool. We also observed poor performance of all tools, with none achieving an F1-score greater than 0.26, and qualitatively different behaviors between general-purpose alternative splicing detection tools and tools confined to retained intron detection.
conclusionsShort-read tools detect intron retention with poor recall and precision, calling into question the completeness and validity of a large percentage of putatively retained introns called by commonly used methods.
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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 Socratic graph.