ArticleBioTechniques2017
Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing.
Article in BioTechniques, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Analytical Validation of Loss of Heterozygosity and Mutation Detection in Pancreatic Fine-Needle Aspirates by Capillary Electrophoresis and Sanger Sequencing.Diagnostics (Basel, Switzerland) · 2024Article
- Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine.BMC biology · 2024Article
- PRO-seq: Precise Mapping of Engaged RNA Pol II at Single-Nucleotide Resolution.Current protocols · 2023Article
- Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of PlasmaGenes · 2023Article
- A Novel Synthetic Oleanolic Acid Derivative Inhibits Glioma Cell Proliferation by Regulating Cell Cycle G2/M Arrest.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Systematic detection of mosaicism by using digital NGS reveals three new MEN1 mosaicisms.Endocrine connections · 2022Article
- Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing.Nature communications · 2022Article
- Increasing the efficiency and precision of prime editing with guide RNA pairs.Nature chemical biology · 2022Article
- High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing.Cell systems · 2021Article
- Tissue-specific transcriptome forPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors.Nature methods · 2021Article
- Technological Approaches in the Analysis of Extracellular Vesicle Nucleotide Sequences.Frontiers in bioengineering and biotechnology · 2021Review
- Currently Applied Molecular Assays for IdentifyingInternational journal of molecular sciences · 2020Review
- Insufficiently complex unique-molecular identifiers (UMIs) distort small RNA sequencing.Scientific reports · 2020Article
- Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics.Journal of clinical medicine · 2020Review
- Identifying a wide range of actionable variants using capture-based ultra-deep targeted sequencing in treatment-naive patients with primary lung adenocarcinoma.International journal of clinical and experimental pathology · 2020Article
- Systematic assessment of commercially available low-input miRNA library preparation kits.RNA biology · 2020Article
- RNA sequencing: the teenage years.Nature reviews. Genetics · 2019Review
- Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods.BMC genomics · 2019Article
- A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory.PLoS computational biology · 2019Article
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Authors and funding
2 authors.
Funding
Abstract
Quantitative analysis of next-generation sequencing (NGS) data requires discriminating duplicate reads generated by PCR from identical molecules that are of unique origin. Typically, PCR duplicates are identified as sequence reads that align to the same genomic coordinates using reference-based alignment. However, identical molecules can be independently generated during library preparation. Misidentification of these molecules as PCR duplicates can introduce unforeseen biases during analyses. Here, we developed a cost-effective sequencing adapter design by modifying Illumina TruSeq adapters to incorporate a unique molecular identifier (UMI) while maintaining the capacity to undertake multiplexed, single-index sequencing. Incorporation of UMIs into TruSeq adapters (TrUMIseq adapters) enables identification of bona fide PCR duplicates as identically mapped reads with identical UMIs. Using TrUMIseq adapters, we show that accurate removal of PCR duplicates results in improved accuracy of both allele frequency (AF) estimation in heterogeneous populations using DNA sequencing and gene expression quantification using 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.