Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA.

ABSTRACT:

Background

Plasma cell-free DNA (cfDNA) is derived from cellular death in various tissues. Investigating the tissue origin of cfDNA through cell type deconvolution, we can detect changes in tissue homeostasis that occur during disease progression or in response to treatment. Consequently, cfDNA has emerged as a valuable noninvasive biomarker for disease detection and treatment monitoring. Although there are many methylation-based methods for cfDNA cell type deconvolution, a comprehensive and systematic evaluation of these methods has yet to be conducted.

Results

In this study, we benchmark five methods: MethAtlas, cfNOMe toolkit, CelFiE, CelFEER, and UXM. Utilizing deep whole-genome bisulfite sequencing data from 35 human cell types, we generate in silico cfDNA samples with

SUBMITTER: Sun T 

PROVIDER: S-EPMC11660681 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature