Reference-free deconvolution of DNA methylation data and mediation by cell composition effects.

ABSTRACT:

Background

Recent interest in reference-free deconvolution of DNA methylation data has led to several supervised methods, but these methods do not easily permit the interpretation of underlying cell types.

Results

We propose a simple method for reference-free deconvolution that provides both proportions of putative cell types defined by their underlying methylomes, the number of these constituent cell types, as well as a method for evaluating the extent to which the underlying methylomes reflect specific types of cells. We demonstrate these methods in an analysis of 23 Infinium data sets from 13 distinct data collection efforts; these empirical evaluations show that our algorithm can reasonably estimate the number of constituent types, return cell proportion estimates that d

SUBMITTER: Houseman EA 

PROVIDER: S-EPMC4928286 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature