BayesAge: A maximum likelihood algorithm to predict epigenetic age

被引:3
作者
Mboning, Lajoyce [1 ]
Rubbi, Liudmilla [2 ]
Thompson, Michael [2 ]
Bouchard, Louis-S. [1 ]
Pellegrini, Matteo [2 ]
机构
[1] Univ Calif Los Angeles, Dept Chem & Biochem, Los Angeles, CA 90095 USA
[2] Univ Calif Los Angeles, Dept Mol Cell & Dev Biol, Los Angeles, CA USA
来源
FRONTIERS IN BIOINFORMATICS | 2024年 / 4卷
关键词
BayesAge; scAge; epigenetic age; maximum likelihood estimation; true age; DNA METHYLATION; BIOMARKER;
D O I
10.3389/fbinf.2024.1329144
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Introduction: DNA methylation, specifically the formation of 5-methylcytosine at the C5 position of cytosine, undergoes reproducible changes as organisms age, establishing it as a significant biomarker in aging studies. Epigenetic clocks, which integrate methylation patterns to predict age, often employ linear models based on penalized regression, yet they encounter challenges in handling missing data, count-based bisulfite sequence data, and interpretation.Methods: To address these limitations, we introduce BayesAge, an extension of the scAge methodology originally designed for single-cell DNA methylation analysis. BayesAge employs maximum likelihood estimation (MLE) for age inference, models count data using binomial distributions, and incorporates LOWESS smoothing to capture non-linear methylation-age dynamics. This approach is tailored for bulk bisulfite sequencing datasets.Results: BayesAge demonstrates superior performance compared to scAge. Notably, its age residuals exhibit no age association, offering a less biased representation of epigenetic age variation across populations. Furthermore, BayesAge facilitates the estimation of error bounds on age inference. When applied to down-sampled data, BayesAge achieves a higher coefficient of determination between predicted and actual ages compared to both scAge and penalized regression.Discussion: BayesAge presents a promising advancement in epigenetic age prediction, addressing key challenges encountered by existing models. By integrating robust statistical techniques and tailored methodologies for count-based data, BayesAge offers improved accuracy and interpretability in predicting age from bulk bisulfite sequencing datasets. Its ability to estimate error bounds enhances the reliability of age inference, thereby contributing to a more comprehensive understanding of epigenetic aging processes.
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页数:11
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