Genetic Ancestry Estimates within Dutch Family Units and Across Genotyping Arrays: Insights from Empirical Analysis Using Two Estimation Methods

Abstract

Accurate inference of genetic ancestry is crucial for population-based association studies, accounting for population heterogeneity and structure. This study analyzes genome-wide SNP data from the Netherlands Twin Register to compare genetic ancestry estimates. The focus is on the comparison of ancestry estimates between family members and individuals genotyped on multiple arrays (Affymetrix 6.0, Affymetrix Axiom, and Illumina GSA). Two conventional methods, principal component analysis and ADMIXTURE, were implemented to estimate ancestry, each serving its specific purpose, rather than for direct comparison. The results reveal that as the degree of genetic relatedness decreases, the Euclidean distances of genetic ancestry estimates between family members significantly increase (empirical p p p = 0.005). This study highlights the utility of current methods in inferring genetic ancestry, emphasizing the importance of reference population composition in determining ancestry estimates.

Keywords

• within-family analysis
• genetic ancestry estimation
• population structure
• principal components analysis (PCA)
• ADMIXTURE