Highlights
- •The same amplicons from the same samples allow to reveal the differences dependent on the DNA methylation analysis methods.
- •There were high degrees of positive correlation between single-base extension and massively parallel sequencing results.
- •Despite high correlations between the two methods, detected DNA methylation status was not identical in most markers.
- •Rather than exploiting integrated models, applying method-specific models would achieve higher accuracy in age prediction.
Abstract
Forensic research surrounding the use of DNA methylation (DNAm) markers to predict
age suggests that accurate prediction of chronological age can be achieved with just
several DNAm markers. Several age-prediction models are based on DNAm levels that
are detectable by a diverse range of DNAm analysis methods. Among the many DNAm analysis
methods, targeted amplicon-based massively parallel sequencing (MPS) and single-base
extension (SBE) methods have been widely studied owing to their practicality, including
their multiplex capabilities. Since these two DNAm analysis methods share an identical
amplification step during their experimental processes, several studies have compared
the differences between the methods to construct integrated age-prediction models
based on both MPS and SBE data. In this study, we compared the specific differences
in DNAm levels between these two commonly exploited analysis methods by analyzing
the identical PCR amplicons from the same samples and quantifying the actual bisulfite-converted
DNA amount involved in the PCR step. The DNAm levels of five well-studied age-associated
markers—CpGs on the ELOVL2, FHL2, KLF14, MIR29B2CHG, and TRIM59 genes—were obtained from blood samples of 250 Koreans using both DNAm analysis methods.
The results showed that only ELOVL2 is interchangeable between the MPS and SBE methods,
while the rest of the markers showed significant differences in DNAm values. These
differences may result in high errors and consequential lowered accuracy in age estimates.
Therefore, a DNAm analysis method-specific approach that considers method-induced
DNAm differences is recommended to improve the overall accuracy and reliability of
age-prediction methods.
Keywords
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Article info
Publication history
Published online: November 09, 2022
Accepted:
November 8,
2022
Received in revised form:
November 2,
2022
Received:
April 15,
2022
Identification
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© 2022 Elsevier B.V. All rights reserved.
