Correcting for relatedness when identifying differentially methylation positions and regions in 450K/EPIC array data

[elainee...@gmail.com]

Hi all,

I am looking for differentially methylated positions and regions within a set of samples that include some known close relatives. The data were generated using the EPIC array. I have mostly been using ChAMP so far to normalize, remove batch effects, etc. However, I have not found a way that I can correct for relatedness in a model to identify DMPs (or DMRs). 

It seems like there are several options for implementing linear mixed models that can correct for relatedness in GWAS (GEMMA, FaST-LMM), as well as a piece of software that accounts for relatedness in a binomial mixed model that is designed to run on bisulfite seq short read count data (MACAU). But I was wondering if anyone had any idea about how to implement something similar in methylation microarray data.

Thank you for any thoughts!

My best,

Elaine