Table 3.

SNP-Heritability Estimates from Different GRM Methods for 2,928 Schizophrenia Cases and 4,373 Controls from the Swedish Genome-wide Association Study Imputed to 1000 Genomes

GRM Method	${\mathit{h}}_{\mathbf{CC}}^{\mathbf{2}}$(SE) Observed Scale	${\mathit{h}}_{\mathbf{SNP}}^{\mathbf{2}}$(SE) Liability Scalea	ΔAICb
Standard GRM with s = −1	0.57 (0.05)	0.33 (0.03)	143.88
Standard GRM with s = 0	0.49 (0.04)	0.28 (0.02)	151.26
Speed et al. weighted GRM	0.79 (0.10)	0.45 (0.06)	61.32
Speed et al. weighted GRM with bufferc = 1,000	0.79 (0.10)	0.45 (0.06)	62.00
MAF-stratified approach	0.52 (0.05)	0.30 (0.03)	148.50

^aAssumes a disease prevalence of 0.01.

^bΔAIC between the null model (no GRM fitted) and the full model. A high ΔAIC indicates a better fit.

^cIn the weighting method, windows of 3,000 SNPs plus buffers of 500 SNPs were used by default in the LDAK software; in this example, the buffer size was increased to 1,000 SNPs.