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Updated: Mar 21, 2026

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
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Evaluating ancestry adjustment in multi-ancestry epigenome-wide analysis.

Yueming Liu1, Alan Kuang1, Marie-France Hivert2,3,4

  • 1Division of Biostatistics and Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.

Epigenetics
|March 20, 2026
PubMed
Summary

Creating new reference sets from multi-ancestry cohorts improves ancestry adjustment in epigenome-wide association studies (EWAS). This enhances the detection of biologically relevant associations for newborn traits.

Keywords:
DNA methylationEPISTRUCTUREancestryepigeneticsepigenome-wide association study (EWAS)

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Area of Science:

  • Genetics
  • Epigenetics
  • Population Genetics

Background:

  • Accurate adjustment for population substructure is crucial in epigenome-wide association studies (EWAS), especially in diverse ancestral cohorts.
  • The EPISTRUCTURE tool, a genotype-free ancestry inference method, was initially validated using a European reference population (KORA).
  • Its performance in multi-ancestry settings requires further evaluation.

Purpose of the Study:

  • To assess the effectiveness of EPISTRUCTURE's principal components (PCs) for ancestry adjustment in EWAS using multi-ancestry cord-blood samples.
  • To compare ancestry adjustment using a standard European (KORA) reference versus novel references derived from the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) cohort.
  • To evaluate the impact of different reference sets on association detection and biological interpretation for newborn adiposity traits.

Main Methods:

  • Systematically evaluated EPISTRUCTURE PCs derived from KORA and HAPO-based reference sets.
  • HAPO reference sets were constructed using varying SNP-CpG R² thresholds (e.g., RS30: R² > 0.3) to identify ancestry-informative CpGs.
  • Applied these references for population substructure adjustment in EWAS of birthweight, cord C-peptide, and sum of skinfolds in HAPO cord blood samples (n=3,116).

Main Results:

  • The HAPO RS30 reference consistently yielded lower genomic inflation compared to the KORA reference.
  • Biologically relevant associations for birthweight and cord blood C-peptide were more frequently identified using the HAPO-derived reference.
  • Pathway enrichment analyses revealed significant immune and metabolic signals, with some pathways uniquely identified using the HAPO reference.

Conclusions:

  • Reference sets generated from multi-ancestry cohorts, such as HAPO, provide superior ancestry adjustment in EWAS.
  • Utilizing ancestry-informative CpGs from diverse populations enhances the detection of true biological associations.
  • This approach improves the reliability and interpretability of EWAS findings in genetically heterogeneous cohorts.