Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies.

ABSTRACT: To distinguish DNA methylation (DNAm) from cell proportion changes in whole placental villous tissue research, we developed a robust cell type-specific DNAm reference to estimate cell composition. We collated new and existing cell type DNAm profiles quantified via Illumina EPIC or 450k microarrays. To estimate cell composition, we deconvoluted whole placental samples (n = 36) with robust partial correlation based on the top 30 hyper- and hypomethylated sites identified per cell type. To test deconvolution performance, we evaluated root mean square error in predicting principal components of DNAm variation in 204 external placental samples. We analyzed DNAm profiles (n = 368,435 sites) from 12 cell types: cytotrophoblasts (n = 18), endothelial cells (n = 19), Hof

SUBMITTER: Campbell KA 

PROVIDER: S-EPMC11633140 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature