A comparison of DMET Plus microarray and genome-wide technologies by assessing population substructure

Area of Science:

• Genomics
• Population Genetics
• Pharmacogenomics

Background:

• Population substructure and cryptic relatedness are critical factors in genomic association studies.
• Accurate estimation of these factors is essential for reliable results.
• The Affymetrix DMET Plus pharmacogenomics genotyping chip is a tool for genetic analysis.

Purpose of the Study:

• To evaluate the Affymetrix DMET Plus pharmacogenomics genotyping chip's ability to estimate population substructure and cryptic relatedness.
• To compare these estimates with those derived from genome-wide HapMap data.

Main Methods:

• Genotypic data were collected from 301 individuals across four populations using the Affymetrix DMET Plus microarray.
• Genome-wide data for the same individuals were obtained from HapMap release 3.
• Population substructure was analyzed using Eigenstrat and ADMIXTURE; cryptic relatedness was assessed via inbreeding coefficients.

Main Results:

• Principal components analysis revealed similar population substructure patterns between DMET Plus and HapMap data.
• ADMIXTURE analysis successfully identified subpopulations in both datasets.
• Nonparametric correlations showed significant associations between the two platforms (average ρ=0.7272), with high concordance in ADMIXTURE results (average ρc=0.9693).
• DMET Plus data showed slightly inflated inbreeding coefficients compared to HapMap data.

Conclusions:

• The DMET Plus chip is effective for quantifying population substructure and inferring admixed populations.
• The microarray provides adequate data depth for covariate adjustment in genomic association studies.
• These findings support the utility of the DMET Plus chip in population genetic analyses relevant to pharmacogenomics.