Optimizing genetic ancestry adjustment in DNA methylation studies: a comparative analysis of approaches.

ABSTRACT:

Background

Genetic ancestry is an important factor to account for in DNA methylation studies because genetic variation influences DNA methylation patterns. One approach uses principal components (PCs) calculated from CpG sites that overlap with common SNPs to adjust for ancestry when genotyping data is not available. However, this method does not remove technical and biological variations, such as sex and age, prior to calculating the PCs. The first PC is therefore often associated with factors other than ancestry.

Methods

We developed and adapted the adapted EpiAnceR+ approach, which includes (1) residualizing the CpG data overlapping with common SNPs for control probe PCs, sex, age, and cell type proportions to remove the effects of technical and biological factors, and (2

SUBMITTER: Hoffler KD 

PROVIDER: S-EPMC12522430 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature