Table 3 Prediction accuracy in simulation studies in which the phenotype is associated with SNPs only (heritability = 0.05).

Distribution of the true SNP effects	Prediction models	Number of true susceptibility variants
		100		200		500		2000		5000
		Mean (SE) PCC	Power^a	Mean (SE) PCC	Power^a	Mean (SE) PCC	Power^a	Mean (SE) PCC	Power^a	Mean (SE) PCC	Power^a
Laplace distribution	STMGP	0.0594 (0.0243)	0.85	0.0440 (0.0311)	0.65	−0.0044 (0.0215)	0.15	0.0143 (0.1939)	0.15	−0.0028 (0.0135)	0.00
	PRS	0.0089 (0.0240)	0.15	0.0094 (0.0187)	0.10	−0.0070 (0.0208)	0.15	0.0059 (0.0173)	0.05	−0.0017 (0.0133)	0.05
	GBLUP	0.0118 (0.0159)	0.05	0.0080 (0.0155)	0.00	0.0067 (0.0210)	0.15	0.0149 (0.0013)	0.05	0.0160 (0.0142)	0.10
	SBLUP	0.0048 (0.0140)	0.00	0.0100 (0.0137)	0.00	0.0083 (0.0198)	0.10	0.0142 (0.0129)	0.05	0.0111 (0.0193)	0.10
	BayesR	0.0391 (0.0494)	0.65	0.0264 (0.0273)	0.30	0.0073 (0.0234)	0.15	0.0144 (0.0142)	0.10	0.0109 (0.0176)	0.10
	Ridge	0.0052 (0.0146)	0.05	0.0049 (0.0155)	0.00	0.0104 (0.0216)	0.15	0.0085 (0.0132)	0.05	0.0072 (0.0172)	0.00
Normal distribution	STMGP	0.0475 (0.0238)	0.70	0.0140 (0.0170)	0.10	0.0082 (0.0197)	0.15	0.0112 (0.0071)	0.10	0.0040 (0.0175)	0.05
	PRS	0.0028 (0.0207)	0.05	0.0054 (0.0191)	0.15	0.0017 (0.0185)	0.05	−0.0011 (0.0189)	0.05	0.0031 (0.0146)	0.10
	GBLUP	0.0120 (0.0135)	0.05	0.0103 (0.0171)	0.05	0.0133 (0.0147)	0.10	0.0127 (0.0199)	0.10	0.0130 (0.0154)	0.10
	SBLUP	0.0117 (0.0177)	0.15	0.0109 (0.0167)	0.05	0.0057 (0.0145)	0.10	0.0068 (0.0155)	0.00	0.0116 (0.0127)	0.05
	BayesR	0.0239 (0.0271)	0.35	0.0147 (0.0185)	0.10	0.0073 (0.0168)	0.10	0.0108 (0.0194)	0.05	0.0092 (0.0133)	0.05
	Ridge	0.0144 (0.0162)	0.20	0.0135 (0.0170)	0.05	0.0083 (0.0185)	0.00	0.0100 (0.0197)	0.05	0.0075 (0.0187)	0.00

PCC predictive correlation coefficient, SE standardized error, STMGP Smooth-Threshold Multivariate Genetic Prediction, PRS polygenic risk scores, GBLUP genomic best linear-unbiased prediction, SBLUP summary-data-based best linear-unbiased prediction, NEG normal–exponential–gamma.
^aPower is the proportion of replicates achieving a significant prediction at P value < 0.05.

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