Table 2.

Optimal Choices of C+T Parameters

Trait	wc	$r_c^2$	INFOT	pT
Breast cancer (BRCA)	2,500	0.2	0.95	2.2×10-4
Rheumatoid arthritis (RA)	200	0.5	0.95	7.5×10-2
Type 1 diabetes (T1D)	10K–50K	0.01	0.90	2.6×10-5
Type 2 diabetes (T2D)	625	0.8	0.95	1.1×10-2
Prostate cancer (PRCA)	10K–50K	0.01	0.90	4.2×10-6
Depression (MDD)	625	0.8	0.95	1.0×10-1
Coronary artery disease (CAD)	526	0.95	0.95	3.5×10-2
Asthma	2,500	0.2	0.90	2.2×10-4

Choice of C+T parameters is based on the maximum AUC in the training set. Hyper-parameters of C+T are the squared correlation threshold $r_c^2$ and the window size w_c of clumping, the p value threshold p_T and the threshold on the quality of imputation INFO_T. Choosing optimal hyper-parameters for C+T use 63%–90% of the individuals reported in Table 1. Resulting predictions of maxCT in the test set are reported in Figure 2.