ArticleMolecular diagnosis & therapy2014
Cytosine deamination is a major cause of baseline noise in next-generation sequencing.
Article in Molecular diagnosis & therapy, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
77 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guideline
- Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA.PloS one · 2015Trial
- Methyltransferase-assisted single duplex sequencing for detecting circulating tumor DNA.EMBO molecular medicine · 2026Article
- Profiling KRAS mutations in whole blood by error-corrected maximum depth sequencing.NPJ precision oncology · 2026Article
- Performance comparison of germline variant calling tools in sporadic disease cohorts.Molecular genetics and genomics : MGG · 2025Article
- Alignment-free unique molecular identifier clustering suppresses sequencing errors for accurate detection of low-frequency DNA variants.Briefings in bioinformatics · 2025Article
- Development of a Clinically Applicable High-Resolution Assay for Sperm Mosaicism.The Journal of molecular diagnostics : JMD · 2025Article
- Recurrent somatic mutation and progerin expression in early vascular aging of chronic kidney disease.Nature aging · 2025Article
- Plasma-based analysis of ERBB2 mutational status by multiplex digital PCR in a large series of patients with metastatic breast cancer.Molecular oncology · 2024Article
- Article
- Comparative Analyses of Targeted Myeloid Cancer Next-Generation Sequencing Panel in Fresh Blood, Bone Marrow and FFPE Material.International journal of molecular sciences · 2024Article
- Characterization and mitigation of artifacts derived from NGS library preparation due to structure-specific sequences in the human genome.BMC genomics · 2024Article
- Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine.BMC biology · 2024Article
- A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection.Frontiers in oncology · 2024Review
- Real-world EGFR testing practices for non-small-cell lung cancer by thoracic pathology laboratories across Europe.ESMO open · 2023Article
- Mapinsights: deep exploration of quality issues and error profiles in high-throughput sequence data.Nucleic acids research · 2023Article
- A critical spotlight on the paradigms of FFPE-DNA sequencing.Nucleic acids research · 2023Review
- Development of a Next-generation Sequencing-based Gene Panel Test to Detect Measurable Residual Disease in Acute Myeloid Leukemia.Annals of laboratory medicine · 2023Article
- Test of the FlashFREEZE unit in tissue samples freezing for biobanking purposes.Cell and tissue banking · 2023Article
- Residual Humidity in Paraffin-Embedded Tissue Reduces Nucleic Acid Stability.International journal of molecular sciences · 2023Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
BACKGROUND AND
objectivesAs next-generation sequencing (NGS) becomes a major sequencing platform in clinical diagnostic laboratories, it is critical to identify artifacts that constitute baseline noise and may interfere with detection of low-level gene mutations. This is especially critical for applications requiring ultrasensitive detection, such as molecular relapse of solid tumors and early detection of cancer. We recently observed a ~10-fold higher frequency of C:G > T:A mutations than the background noise level in both wild-type peripheral blood and formalin-fixed paraffin-embedded samples. We hypothesized that these might represent cytosine deamination events, which have been seen using other platforms.
methodsTo test this hypothesis, we pretreated samples with uracil N-glycosylase (UNG). Additionally, to test whether some of the cytosine deamination might be a laboratory artifact, we simulated the heat associated with polymerase chain reaction thermocycling by subjecting samples to thermocycling in the absence of polymerase. To test the safety of universal UNG pretreatment, we tested known positive samples treated with UNG.
resultsUNG pretreatment significantly reduced the frequencies of these mutations, consistent with a biologic source of cytosine deamination. The simulated thermocycling-heated samples demonstrated significantly increased frequencies of C:G > T:A mutations without other baseline base substitutions being affected. Samples with known mutations demonstrated no decrease in our ability to detect these after treatment with UNG.
conclusionBaseline noise during NGS is mostly due to cytosine deamination, the source of which is likely to be both biologic and an artifact of thermocycling, and it can be reduced by UNG pretreatment.
Indexed as
Identifiers
What OpenQuestion holds
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.