Table 2. Significant association of deletions at 1q21.1, 15q11.2 and 15q13.3 with schizophrenia and related psychoses in the combined samples.

Locus	Chromosome 1: 144.94-146.29 (Mb)		Chromosome 15: 20.31-20.78 (Mb)		Chromosome 15: 28.72-30.30 (Mb)
	Cases	Controls	Cases	Controls	Cases	Controls
Germany	2 of 911	0 of 1,297	3 of 911	4 of 1,297	0 of 911	0 of 1,297
Scotland	2 of 451	0 of 441	5 of 451	1 of 441	0 of 451	0 of 441
The Netherlands	0 of 806	0 of 4,039	4 of 806	12 of 4,039	3 of 806	1 of 4,039
Norway	0 of 237	0 of 272	0 of 237	0 of 272	1 of 237	0 of 272
Denmark*	3 of 442	0 of 1,437	4 of 442	3 of 1,432	0 of 375	0 of 501
China*	0 of 438	0 of 463	0 of 438	0 of 463	NA	NA
Phase II
OR		∞ (2.85, ∞)		2.18 (1.01, 4.60)		16.47 (1.52, 833.38)
P-value		5.6×10−4		0.032		7.9×10−3
Phase I and II
OR		14.83 (3.55, 60.40)		2.73 (1.50, 4.89)		11.54 (2.53, 49.58)
P-value		2.9×10−5		6.0×10−4		5.3×10−4

The three deletions nominally significant in phase I were tested for association in follow up samples from Germany, Scotland, The Netherlands, Denmark, Norway and China. All three deletions associate with schizophrenia and related psychoses in the combined phase I and II samples (the multiple testing significance threshold is 0.05/66=7.6×10⁻⁴). P-values in the table (uncorrected for the 66 tests) are from the exact Cochran-Mantel-Haenszel test and are two-sided. Coordinates are based on Build 36 assembly of the human genome. 95% confidence intervals are given within brackets. NA, not analysed.

^*Samples were measured using Taqman assays. Samples with CNVs identified by measuring gene dosage by a Taqman assay were verified and confirmed by genotyping the respective samples using the HumanCNV370 chip. A limited amount of DNA was available for genotyping the Chinese samples.