Fig. 2

Comparison of prediction performance of four methods using individuals and SNPs common between gChip and iChip. The sample consisted of 2479 cases and 3440 controls for CD and 2357 cases and 6740 controls for UC. The number of SNPs was 42,534. Prediction accuracy is measured as the area under the curve (AUC) with higher values denoting better performance. Vertical lines display the variation of estimates in 5-fold cross-validation. Prediction models were trained using either disease status (0–1) or disease phenotype adjusted for ancestry (adjusted)