A novel method for cell deconvolution using DNA methylation in PCA space.

ABSTRACT:

Background

In this study, we present a novel method for reference-based cell deconvolution using data from DNA methylation arrays. Different from existing methods like IDOL-Ext, which operate on probe-level data, our approach represents features in the principal component analysis (PCA) space for cell type deconvolution.

Results

Our method's accuracy in estimating cell compositions is validated across various public datasets, including blood samples from glioma patients. It demonstrates precision comparable to IDOL-Ext, with R² values ranging from 0.73 to 0.99 for most cell types, while offering improved discrimination between similar cell types, particularly T cell subtypes in glioma patient samples (R² 0.42-0.75 vs. 0.36-0.66 for IDOL-Ext). However, b

SUBMITTER: Xu H 

PROVIDER: S-EPMC11344294 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature