ArticleBMC genomics2018
Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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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.
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Who cites it
106 citing papers in PubMed.
- Unique circulating miRNAome signatures captured with distinct molecular states in Lynch syndrome and sporadic colorectal cancer.Molecular oncology · 2026Article
- Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline.Bioinformatics (Oxford, England) · 2026Article
- Network-based analysis reveals potential microRNA regulation of oncogenic pathways in SOX10-depleted uveal melanoma.Cellular and molecular life sciences : CMLS · 2026Article
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- Beyond miRNA Cargo Profiles: Anti-Inflammatory Roles of Extracellular Vesicle-Enriched miRNAs Derived From Human Intervertebral Disc Cells Unveiled by Functional Testing.Journal of extracellular biology · 2026Article
- A metrological foundation for absolute transcriptomics using International System of Units-anchored calibrators.Nature communications · 2026Article
- Molecular profiling of glioblastoma-derived extracellular vesicles identifies small nucleolar RNAs as candidate liquid biomarkers for radiation- induced senescence.bioRxiv : the preprint server for biology · 2026Article
- An absolute quantification atlas of small non-coding RNAs across diverse mammalian tissues and cell lines.Nature communications · 2026Article
- Advances in Massive Parallel Sequencing: From Genomics to Spatial Transcriptomics.Advances in experimental medicine and biology · 2026Review
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- Optimizing Small RNA Sequencing for Salivary Biomarker Identification: A Comparative Study of Library Preparation Protocols.International journal of molecular sciences · 2025Article
- Optimization and Evaluation of the bestRAD Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, Bactrocera dorsalis.Molecular ecology resources · 2025Article
- How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads.Quantitative biology (Beijing, China) · 2025Review
- Genomic Insights into Tumorigenesis in Newly Diagnosed Multiple Myeloma.Diagnostics (Basel, Switzerland) · 2025Article
- Absolute quantification of mammalian microRNAs for therapeutic RNA cleavage and detargeting.RNA (New York, N.Y.) · 2025Article
- The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers.Genome biology · 2025Article
- Article
- Article
- All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies.Nature reviews. Molecular cell biology · 2025Review
- Construction of edit-distance graphs for large sets of short reads through minimizer-bucketing.Bioinformatics advances · 2025Article
46 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundRNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules.
resultsWe have incorporated UMIs into RNA-seq and small RNA-seq protocols and developed tools to analyze the resulting data. Our UMIs contain stretches of random nucleotides whose lengths sufficiently capture diverse molecule species in both RNA-seq and small RNA-seq libraries generated from mouse testis. Our approach yields high-quality data while allowing unique tagging of all molecules in high-depth libraries.
conclusionsUsing simulated and real datasets, we demonstrate that our methods increase the reproducibility of RNA-seq and small RNA-seq data. Notably, we find that the amount of starting material and sequencing depth, but not the number of PCR cycles, determine PCR duplicate frequency. Finally, we show that computational removal of PCR duplicates based only on their mapping coordinates introduces substantial bias into data analysis.
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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.