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Related Concept Videos

Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

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Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).
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To learn more about the function of a gene, researchers can observe what happens when the gene is inactivated or “knocked out,” by creating genetically engineered knockout animals. Knockout mice have been particularly useful as models for human diseases such as cancer, Parkinson’s disease, and diabetes.
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Related Experiment Video

Updated: Sep 14, 2025

CometChip: A High-throughput 96-Well Platform for Measuring DNA Damage in Microarrayed Human Cells
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Genome-wide mutation analysis induced by mutagens in TK6 cells using Hawk-Seq™.

Yuki Otsubo1, Takako Hirose1, Shoji Matsumura1

  • 1R&D -Safety Science Research, Kao Corporation, 3-25-14 Tono-machi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-0821, Japan.

Mutation Research. Genetic Toxicology and Environmental Mutagenesis
|July 24, 2025
PubMed
Summary

Error-corrected next-generation sequencing (ecNGS) using Hawk-Seq™ effectively identified chemical-induced mutations in human cells. This method significantly reduced background noise, improving the detection of rare genetic alterations.

Keywords:
Error-corrected next-generation sequencingGenome-wide mutation analysisHawk-Seq™Rare variantsTK6

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Area of Science:

  • Genomics
  • Toxicology
  • Molecular Biology

Background:

  • Error-corrected next-generation sequencing (ecNGS) is crucial for detecting rare mutations.
  • Clonal and sub-clonal variants (CVs and SCVs) can reduce mutation detection sensitivity in sequencing studies.
  • The TK6 human lymphoblastoid cell line is a standard model for genotoxicity testing.

Purpose of the Study:

  • To apply Hawk-Seq™ for evaluating chemical-induced mutations in TK6 cells.
  • To identify and filter out clonal and sub-clonal variants to improve mutation detection sensitivity.
  • To establish a reliable method for assessing mutagenicity of chemicals like MNU and ENU.

Main Methods:

  • Resequencing of the TK6 genome to identify 4,501,430 clonal variants (CVs).
  • Filtering of common base substitutions (BSs) across vehicle controls to identify and remove sub-clonal variants (SCVs).
  • Application of Hawk-Seq™ to TK6 cells treated with N-methyl-N-nitrosourea (MNU) and N-ethyl-N-nitrosourea (ENU) after rigorous background filtering.

Main Results:

  • Initial BS frequency in vehicle controls was 2.0 × 10-6 bp, reduced to 0.65 × 10-6 bp after filtering CVs and SCVs.
  • MNU treatment resulted in a BS frequency of 9.0 × 10-6 bp, predominantly G:C > A:T mutations.
  • ENU treatment showed a BS frequency of 2.0 × 10-6 bp, with increased G:C > A:T, A:T > C:G, and A:T > G:C mutations.

Conclusions:

  • The developed method using Hawk-Seq™ with CV/SCV filtering significantly enhances the signal-to-noise ratio for mutation detection.
  • The method accurately identified distinct mutagenic profiles for MNU and ENU, reflecting their known mechanisms.
  • This approach holds potential for sensitive detection of mutations and elucidation of diverse mutagenic mechanisms in toxicological studies.