Identifying heterogeneous transgenerational DNA methylation sites via clustering in beta regression

TL;DR

This study introduces a clustering method using beta regression and EM algorithm to identify heterogenous transgenerational DNA methylation sites, revealing paternal and maternal transmission patterns in methylation data.

Contribution

The paper presents a novel clustering approach with beta regression and EM algorithm for identifying transgenerational methylation sites at the population level.

Findings

Identified CpG sites with paternal methylation transmission.

Detected CpG sites mainly maternally transmitted.

Applied method to 4063 CpG sites in 41 triads.

Abstract

This paper explores the transgenerational DNA methylation pattern (DNA methylation transmitted from one generation to the next) via a clustering approach. Beta regression is employed to model the transmission pattern from parents to their offsprings at the population level. To facilitate this goal, an expectation maximization algorithm for parameter estimation along with a BIC criterion to determine the number of clusters is proposed. Applying our method to the DNA methylation data composed of 4063 CpG sites of 41 mother-father-infant triads, we identified a set of CpG sites in which DNA methylation transmission is dominated by fathers, while at a large number of CpG sites, DNA methylation is mainly maternally transmitted to the offspring.