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Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
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Profiling age and body fluid DNA methylation markers using nanopore adaptive sampling.

Zaka Wing-Sze Yuen1, Somasundhari Shanmuganandam2, Maurice Stanley2

  • 1EMBL Australia Partner Laboratory Network, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; The Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; The Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australia.

Forensic Science International. Genetics
|April 19, 2024
PubMed
Summary

This study introduces nanopore adaptive sampling for simultaneous DNA methylation analysis. This method accurately identifies age and body fluid markers, discovering new age-associated sites.

Keywords:
Age markersBody fluid markersDNA methylationNanopore adaptive samplingNanopore sequencingPCR-freeSequencingTargeted

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Area of Science:

  • Epigenetics and Genomics
  • Biomarker Discovery
  • Molecular Biology

Background:

  • DNA methylation is crucial for development, gene expression, and aging.
  • Current methods target methylation markers individually, lacking a unified approach.
  • Diverse technologies exist for methylation detection and profiling.

Purpose of the Study:

  • To evaluate nanopore adaptive sampling for simultaneous identification of age and body fluid methylation markers.
  • To assess the feasibility of a single technology for multiplexed methylation profiling.
  • To explore novel age-associated methylation markers.

Main Methods:

  • Utilized nanopore adaptive sampling for DNA methylation analysis.
  • Focused on simultaneous profiling of age-associated and body fluid-specific CpG sites.
  • No specialized DNA preparation or additional biochemical treatments were required.

Main Results:

  • Adaptive sampling provided sufficient coverage for accurate methylation status determination.
  • Results showed strong consistency with whole-genome bisulfite sequencing data.
  • Confirmed known CpG markers for age and body fluid identification.
  • Identified novel CpG sites strongly correlated with age.

Conclusions:

  • Nanopore adaptive sampling is a feasible and effective method for multiplexed DNA methylation analysis.
  • This approach supports the development of unified assays for age prediction and body fluid identification.
  • Further validation and expansion of this methodology are warranted.