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Can we integrate method-specific age-predictive models?: Analysis method-induced differences in detected DNA

Sae Rom Hong1, Kyoung-Jin Shin1

  • 1Department of Forensic Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50-1 Yonsei-ro, 03722 Seoul, Republic of Korea.

Forensic Science International. Genetics
|November 15, 2022
PubMed
Summary
This summary is machine-generated.

DNA methylation (DNAm) analysis methods like massively parallel sequencing (MPS) and single-base extension (SBE) show significant differences for age prediction markers. Method-specific approaches are crucial for accurate forensic age estimation.

Keywords:
Age correlationDNA methylationMassively parallel sequencingMultiplex PCRSingle-base extension

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Area of Science:

  • Forensic Science
  • Epigenetics
  • Molecular Biology

Background:

  • DNA methylation (DNAm) markers are promising for predicting chronological age.
  • Massively parallel sequencing (MPS) and single-base extension (SBE) are practical DNAm analysis methods.
  • These methods share an amplification step, prompting comparisons for integrated age-prediction models.

Purpose of the Study:

  • To compare DNA methylation levels between MPS and SBE methods using identical PCR amplicons.
  • To quantify differences in DNA methylation values for specific age-associated markers.
  • To assess the impact of method-induced differences on age-prediction accuracy.

Main Methods:

  • Analyzed DNA methylation levels of five age-associated markers (ELOVL2, FHL2, KLF14, MIR29B2CHG, TRIM59) in 250 Korean blood samples.
  • Utilized both targeted amplicon-based massively parallel sequencing (MPS) and single-base extension (SBE) methods.
  • Quantified bisulfite-converted DNA amounts during the PCR step.

Main Results:

  • Only the ELOVL2 marker showed interchangeable DNA methylation values between MPS and SBE methods.
  • Significant differences in DNA methylation values were observed for FHL2, KLF14, MIR29B2CHG, and TRIM59.
  • These discrepancies can lead to substantial errors and reduced accuracy in age estimation.

Conclusions:

  • DNA methylation analysis methods are not interchangeable for all age-prediction markers.
  • Method-specific DNA methylation differences must be considered for reliable age estimation.
  • A DNAm analysis method-specific approach is recommended to enhance the accuracy of forensic age-prediction models.