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Table 1 Differences in allele frequencies between African and European populations for different genotyping technologies

From: Genetic disease risks can be misestimated across global populations

Data type Allele frequency difference between Africa and Europe
Ancestral risk allele (%) Derived risk allele (%)
NHGRI-EBI GWAS Catalog (empirical) + 11.7 − 6.7
Affymetrix Genome-Wide Human SNP Array 6.0 (simulated)* + 10.7 − 8.0
Illumina Omni 5M microarray (simulated)* + 11.0 − 8.2
Whole genome sequences (simulated)* + 9.7 − 7.2
  1. *GWAS simulation parameters: sample size = 3500 cases and 3500 controls, study population = EUR, p value threshold = 1 × 10−5, mode of inheritance = additive, prevalence = 0.1, genotype relative risk = 1.211