Table 3.
Areas under the curve for all scores in the training and test data
| SNP selection | Score | AUC train (95 % CI) | AUC test (95 % CI) |
|---|---|---|---|
| 0.012 % | Allele count | 0.9075 (0.8898; 0.9252) | 0.8644 (0.8320; 0.8968) |
| (63 SNPs) | LogOR | 0.8824 (0.8617; 0.9030) | 0.8565 (0.823; 0.8900) |
| LogReg | 0.9449 (0.9321; 0.9577) | 0.8492 (0.8152; 0.8831) | |
| Lasso | 0.9433 (0.9303; 0.9563) | 0.8511 (0.8174; 0.8849) | |
| RJ-Reg | 1.0000 (0.9999; 1.0000) | 0.8883 (0.8599; 0.9167) | |
| 0.025 % | Allele count | 0.8964 (0.8770; 0.9158) | 0.8527 (0.8189; 0.8866) |
| (125 SNPs) | LogOR | 0.8602 (0.8373; 0.8832) | 0.8326 (0.7966; 0.8686) |
| Lasso | 0.9573 (0.9464; 0.9683) | 0.8604 (0.8279; 0.8928) | |
| RJ-Reg | 1.0000 (0.9999; 1.0000) | 0.8877 (0.8591; 0.9163) | |
| 0.049 % | Allele count | 0.9288 (0.9132; 0.9444) | 0.8510 (0.8168; 0.8852) |
| (249 SNPs) | LogOR | 0.8733 (0.8515; 0.8950) | 0.8374 (0.8019; 0.8729) |
| Lasso | 0.9824 (0.9763; 0.9885) | 0.8622 (0.8298; 0.8945) | |
| RJ-Reg | 1.0000 (1.0000; 1.0000) | 0.8925 (0.8644; 0.9206) | |
| 0.098 % | Allele count | 0.9548 (0.9436; 0.9660) | 0.8565 (0.8230; 0.8900) |
| (496 SNPs) | LogOR | 0.8884 (0.8682; 0.9085) | 0.8426 (0.8076; 0.8775) |
| Lasso | 0.9960 (0.9939; 0.9981) | 0.8555 (0.8228; 0.8882) | |
| RJ-Reg | 1.0000 (1.0000; 1.0000) | 0.8914 (0.8631; 0.9198) | |
| 0.196 % | Allele count | 0.9742 (0.9659; 0.9824) | 0.8248 (0.7881; 0.8615) |
| (991 SNPs) | LogOR | 0.9092 (0.8913; 0.9271) | 0.8429 (0.8080; 0.8778) |
| Lasso | 0.9987 (0.9979; 0.9996) | 0.8495 (0.8155; 0.8834) | |
| RJ-Reg | 1.0000 (1.0000; 1.0000) | 0.8902 (0.8617; 0.9188) | |
| 0.782 % | Allele count | 0.9075 (0.8898; 0.9252) | 0.7251 (0.6803; 0.7700) |
| (3960 SNPs) | LogOR | 0.9616 (0.9513; 0.9719) | 0.8456 (0.8110; 0.8802) |
| Lasso | 1.0000 (1.0000; 1.0000) | 0.8477 (0.8136; 0.8817) | |
| RJ-Reg | 1.0000 (1.0000; 1.0000) | 0.8919 (0.8634; 0.9203) | |
| 3.125 % | Allele count | 0.9967 (0.9950; 0.9984) | 0.6474 (0.5988; 0.6961) |
| (15,835 SNPs) | LogOR | 0.9982 (0.9970; 0.9982) | 0.8340 (0.7977; 0.8340) |
| Lasso | 1.0000 (0.9999–1.0000) | 0.8586 (0.8257; 0.8916) | |
| RJ-Reg | 1.0000 (1.0000; 1.0000) | 0.8829 (0.8534; 0.9124) | |
| 12.5 % | LogOR | 1.0000 (1.0000; 1.0000) | 0.7984 (0.7590; 0.8378) |
| (63,334 SNPs) | RJ-Reg | 1.0000 (1.0000; 1.0000) | 0.8854 (0.8563; 0.9146) |
AUC area under the curve, CI confidence interval, Lasso least absolute shrinkage and selection operator, RJ-Reg Random Jungle regression
Allele count: score constructed based on number of risk alleles
LogOR: score constructed by weighting variants with respective log odds ratio from single marker analyses
LogReg: score constructed from logistic regression