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DNA methylation and machine learning: challenges and perspective toward enhanced clinical diagnostics

E. Aref-Eshghi,Arash B. Abadi,Mohammad-Erfan Farhadieh,Amirreza Hooshmand,F. Ghasemi,Leila Youssefian,H. Vahidnezhad,Taylor Martin Kerrins,Xiaonan Zhao,Mahdi Akbarzadeh,H. Hakonarson,A. Saeidian

Published 2025 in Clinical Epigenetics

ABSTRACT

DNA methylation is an epigenetic modification that regulates gene expression by adding methyl groups to DNA, affecting cellular function and disease development. Machine learning, a subset of artificial intelligence, analyzes large datasets to identify patterns and make predictions. Over the past two decades, advances in bioinformatics technologies for arrays and sequencing have generated vast amounts of data, leading to the widespread adoption of machine learning methods for analyzing complex biological information for medical problems. This review explores recent advancements in DNA methylation studies that leverage emerging machine learning techniques for more precise, comprehensive, and rapid patient diagnostics based on DNA methylation markers. We present a general workflow for researchers, from clinical research questions to result interpretation and monitoring. Additionally, we showcase successful examples in diagnosing cancer, neurodevelopmental disorders, and multifactorial diseases. Some of these studies have led to the development of diagnostic platforms that have entered the global healthcare market, highlighting the promising future of this field.

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