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

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.