Aim: To develop a method for estimating cell-specific effects in epigenomic association studies in the presence of cell type heterogeneity.
Materials & methods: We utilized Monte Carlo Expectation-Maximization algorithm with Metropolis-Hastings sampler to reconstruct the ‘missing’ cell-specific methylations and to estimate their associations with phenotypes free of confounding by cell type proportions.
Results: Simulations showed reliable performance of the method under various settings including when the cell type is rare. Application to a real dataset recapitulated the directly measured cell-specific methylation pattern in whole blood.
Conclusion: This work provides a framework to identify important cell groups and account for cell type composition useful for studying the role of epigenetic changes in human traits and diseases.