. Author manuscript; available in PMC: 2016 Sep 22.

Published in final edited form as: Mol Psychiatry. 2016 Jan 12;21(10):1391–1399. doi: 10.1038/mp.2015.197

Table 3.

Results of leave-one-out cross-validation analyses

	Case-Control			Factor Score
Testing Sample	N_SNP^a P_training<10⁻⁵	N_SNP^b P_testing<0.05	N_SNP (same direction)	N_SNP^a P_training<10⁻⁵	N_SNP^b P_testing<0.05	N_SNP (same direction)
MGS	19	3	10	39	0	25
GSK	26	3	12	22	4	11
RS1	24	0	13	42	6	36
RS2	15	3	9	45	0	33
RS3	22	0	10	46	21	35
SHIP	24	0	14	40	10	32
NTR/NESDA^c	14	3	13	-	-	-
QIMR	13	3	9	35	0	32
TRAILS	16	3	13	46	2	41
OVERALL	173	18^* (P=0.001)	103^* (P=0.005)	315	43^* (P<0.001)	245^* (P<0.001)

P<0.05 thresholds applied for replication and sign tests; Replication and sign tests are conducted based on permutations with 9,000 iterations in case-control and 8,000 iterations in factor score phenotype under the null hypothesis of no association (1,000 iteration for each pair of training and testing sets).

The number of SNPs associated at P_training<1×10⁻⁵ with r²<0.4 in the leave-one-out meta-analysis using N-1 training samples after removing one testing sample at a time.

Of the SNPs with P_training<1×10⁻⁵ in the meta-analysis of the N-1 training samples, the number of replicated SNPs with one-sided P_testing<0.05 in the left-out (testing) sample.

Only case-control phenotype is available for NTR/NESDA sample.