Quantitative comparison of within-sample heterogeneity scores for DNA methylation data.

ABSTRACT: DNA methylation is an epigenetic mark with important regulatory roles in cellular identity and can be quantified at base resolution using bisulfite sequencing. Most studies are limited to the average DNA methylation levels of individual CpGs and thus neglect heterogeneity within the profiled cell populations. To assess this within-sample heterogeneity (WSH) several window-based scores that quantify variability in DNA methylation in sequencing reads have been proposed. We performed the first systematic comparison of four published WSH scores based on simulated and publicly available datasets. Moreover, we propose two new scores and provide guidelines for selecting appropriate scores to address cell-type heterogeneity, cellular contamination and allele-specific methylation. Most of the measu

SUBMITTER: Scherer M 

PROVIDER: S-EPMC7192612 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature