Table 1 Prediction accuracies for GAUDI, PRSice and PRS-CSx for the five traits that GAUDI shows higher average R2 compared to PRS-CSx in UKB quantitative serum and urine biomarker trait screening

From: Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-differential effects via GAUDI

Phenotype

GAUDI R2 Mean (sd)

PRSice R2 Mean (sd)

PRS-CSx R2 Mean (sd)

Lipoprotein A

0.092 (0.051)

4.6E-4 (3.5E-4)

3.0E-3 (2.8E-3)

Direct Bilirubin

0.021 (8.9E-3)

3.0E-3 (4.7E-3)

1.2E-4 (7.3E-5)

Total Bilirubin

0.038 (0.013)

4.8E-4 (5.0E-4)

4.5E-4 (4.2E-4)

Apolipoprotein B

0.050 (0.017)

0.016 (0.031)

0.026 (2.9E-3)

LDL direct

0.032 (4.8E-3)

4.8E-4 (2.3E-4)

0.030 (4.3E-3)

  1. We note that GAUDI and PRSice constructed PRS using the same training samples (N ~ 7000), while PRS-CSx additionally leveraged large scale UKB EUR GWAS (N ~ 430,000). The R2 was calculated as the average of the five-fold outer-loop cross-validation R2. Comparison for a complete list of traits is provided in Supplementary Data 2.
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