Detection of cell-type-specific differentially methylated regions in epigenome-wide association studies

TL;DR

This paper introduces a new method to detect cell-type-specific DNA methylation changes in large-scale studies, improving accuracy by considering the spatial relationships between DNA sites.

Contribution

FineDMR is a novel Bayesian method that improves cell-type-specific association detection by leveraging spatial dependencies between CpG sites.

Findings

FineDMR improves power in detecting cell-type-specific associations compared to existing methods.

The method provides both cell-type-specific association detection and methylation profiles for each subject.

Simulation and real data analysis confirm the effectiveness of FineDMR in EWAS data.

Abstract

DNA methylation at cytosine–phosphate–guanine (CpG) sites is one of the most important epigenetic markers. Therefore, epidemiologists are interested in investigating DNA methylation in large cohorts through epigenome-wide association studies (EWAS). However, the observed EWAS data are bulk data with signals aggregated from distinct cell types. Deconvolution of cell-type-specific signals from EWAS data is challenging because phenotypes can affect both cell-type proportions and cell-type-specific methylation levels. Recently, there has been active research on detecting cell-type-specific risk CpG sites for EWAS data. However, existing methods all assume that the methylation levels of different CpG sites are independent and perform association detection for each CpG site separately. Although these methods significantly improve the detection at the aggregated-level—identifying a CpG site as a risk CpG site as long as it is associated with the phenotype in any cell type, they have low power in detecting cell-type-specific associations for EWAS with typical sample sizes.

Here, we develop a new method, Fine-scale inference for Differentially Methylated Regions (FineDMR), to borrow strengths of nearby CpG sites to improve the cell-type-specific association detection. Via a Bayesian hierarchical model built upon Gaussian process functional regression, FineDMR takes advantage of the spatial dependencies between CpG sites. FineDMR can provide cell-type-specific association detection as well as output subject-specific and cell-type-specific methylation profiles for each subject. Simulation studies and real data analysis show that FineDMR substantially improves the power in detecting cell-type-specific associations for EWAS data.

FineDMR is freely available at https://github.com/JiaRuofan/Detection-of-Cell-type-specific-DMRs-in-EWAS.

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