ArticleNucleic acids research2014
Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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
20 citing papers in PubMed, 31 citations in OpenAlex.
- Next-Generation Sequencing Methods to Determine the Accuracy of Retroviral Reverse Transcriptases: Advantages and Limitations.Viruses · 2025Review
- Unique Molecular Identifiers and Multiplexing Amplicons Maximize the Utility of Deep Sequencing To Critically Assess Population Diversity in RNA Viruses.ACS infectious diseases · 2022Article
- A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data.Briefings in bioinformatics · 2021Article
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- The Comparison of Two Single-cell Sequencing Platforms: BD Rhapsody and 10x Genomics Chromium.Current genomics · 2020Review
- Short Communication: HIV-DRLink: A Tool for Reporting Linked HIV-1 Drug Resistance Mutations in Large Single-Genome Data Sets Using the Stanford HIV Database.AIDS research and human retroviruses · 2020Article
- smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers.Bioinformatics (Oxford, England) · 2019Article
- Barcode-free next-generation sequencing error validation for ultra-rare variant detection.Nature communications · 2019Article
- Article
- Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations.Nature reviews. Genetics · 2018Review
- The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules.Scientific reports · 2017Article
- Technical Advances in the Measurement of Residual Disease in Acute Myeloid Leukemia.Journal of clinical medicine · 2017Review
- MtDNA As a Cancer Marker: A Finally Closed Chapter?Current genomics · 2017Review
- Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA.Retrovirology · 2016Article
- Short Communication: Analysis of Minor Populations of Human Immunodeficiency Virus by Primer Identification and Insertion-Deletion and Carry Forward Correction Pipelines.AIDS research and human retroviruses · 2016Article
- Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations.PloS one · 2016Article
- Practical guidelines for B-cell receptor repertoire sequencing analysis.Genome medicine · 2015Review
- Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations.Journal of virology · 2015Article
- Article
- MT-Toolbox: improved amplicon sequencing using molecule tags.BMC bioinformatics · 2014Article
Corrections and comments
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
Abstract
Primer IDs (pIDs) are random oligonucleotide tags used in next-generation sequencing to identify sequences that originate from the same template. These tags are produced by degenerate primers during the reverse transcription of RNA molecules into cDNA. The use of pIDs helps to track the number of RNA molecules carried through amplification and sequencing, and allows resolution of inconsistencies between reads sharing a pID. Three potential issues complicate the above applications. First, multiple cDNAs may share a pID by chance; we found that while preventing any cDNAs from sharing a pID may be unfeasible, it is still practical to limit the number of these collisions. Secondly, a pID must be observed in at least three sequences to allow error correction; as such, pIDs observed only one or two times must be rejected. If the sequencing product contains copies from a high number of RT templates but produces few reads, our findings indicate that rejecting such pIDs will discard a great deal of data. Thirdly, the use of pIDs could influence amplification and sequencing. We examined the effects of several intrinsic and extrinsic factors on sequencing reads at both the individual and ensemble level.
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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.