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. Author manuscript; available in PMC: 2024 Mar 27.
Published in final edited form as: Genet Epidemiol. 2012 May 29;36(5):517–524. doi: 10.1002/gepi.21644

TABLE II.

Association and prediction for polygenic risk scores in relation to PanCa using fourfold CV and varying the r2 threshold for LD pruning

SNP set CV set Number of SNPs in PRSa ORb 95% CI P R 2 c AUC
All SNPs 1 124,754 1.06 0.96–1.18 0.25 0.011 0.559
2 123,874 1.16 1.05–1.29 0.01 0.018 0.574
3 124,038 1.15 1.03–1.27 0.01 0.009 0.555
4 125,106 1.09 0.98–1.21 0.10 0.011 0.562
Pairwise r2 < 0.5 1 56,999 1.10 0.99–1.23 0.07 0.012 0.566
2 56,817 1.14 1.03–1.26 0.02 0.017 0.572
3 56,410 1.18 1.06–1.32 0.00 0.011 0.559
4 57,281 1.09 0.99–1.21 0.10 0.011 0.560
Pairwise r2 < 0.2 1 23,808 1.11 1.00–1.23 0.06 0.012 0.564
2 23,703 1.15 1.04–1.28 0.01 0.017 0.572
3 23,728 1.16 1.05–1.29 0.01 0.010 0.555
4 23,915 1.14 1.02–1.26 0.02 0.013 0.569
a

The P-value threshold for selecting SNPs from the training set was 0.25.

b

ORs based on PRS that has been divided by its standard deviation to generate ORs that correspond to a one standard deviation change in the PRS.

c

Generalized R2 measure for the fitted logistic model.

PRS, polygenic risk score; CV, cross-validation; OR, odds ratio; CI, confidence interval; AUC, area under the curve.