Table 1. Effect of gender stratification on schizophrenia CNV associations.
| Locus | NCNV in cases (Frequency, % in males/% in females) | NCNV in controls (Frequency, % in males/% in females) | SCZ association |
SCZ association controlled for gender |
||
|---|---|---|---|---|---|---|
| Odds Ratio (95% CI) | P-value (two-sided Fisher’s Exact test) | Odds Ratio (95% CI) | P-value (two-sided Cochran-Mantel-Haenszel Exact test) | |||
| 15q11.2 del§ | 84 (0.57/0.78) | 73 (0.43/0.39) | 1.55 (1.12–2.16) | 0.0074 | 1.59 (1.14–2.22) | 0.0050 |
| 15q13.3 del§ | 17 (0.14/0.10) | 4 (0.01/0.03) | 5.73 (1.87–23.39) | 0.00053 | 5.66 (1.81–23.47) | 0.00062 |
| 16p11.2 distal del* | 5 (0.02/0.07) | 4 (0.01/0.03) | 1.68 (0.36–8.48) | 0.51 | 2.12 (0.44–10.95) | 0.30 |
| 16p11.2 dup§ | 42 (0.31/0.34) | 5 (0.02/0.03) | 11.33 (4.49–36.68) | 3.29 × 10−11 | 11.66 (4.57–38.08) | 7.11 × 10−11 |
| 16p13.11 dup§ | 42 (0.25/0.46) | 40 (0.19/0.25) | 1.41 (0.89–2.24) | 0.12 | 1.55 (0.97–2.48) | 0.065 |
| 17p12 del* | 9 (0.03/0.15) | 7 (0.01/0.07) | 1.73 (0.57–5.47) | 0.32 | 2.33 (0.76–7.50) | 0.11 |
| 17q12 del* | 2 (0.00/0.05) | 0 (0.00/0.00) | NA (0.25–∞) | 0.18 | NA (0.41–∞) | 0.097 |
| 1q21.1 del§ | 24 (0.16/0.22) | 6 (0.03/0.03) | 5.39 (2.15–16.13) | 4.80 × 10−5 | 5.64 (2.21–17.10) | 3.77 × 10−5 |
| 1q21.1 dup§ | 16 (0.10/0.17) | 8 (0.02/0.07) | 2.69 (1.09–7.27) | 0.022 | 3.11 (1.23–8.53) | 0.0097 |
| 3q29 del§ | 10 (0.05/0.12) | 0 (0.00/0.00) | NA (3.02–∞) | 0.00020 | NA (3.46–∞) | 0.00010 |
| 22q11.2 del§ | 48 (0.32/0.46) | 0 (0.00/0.00) | NA (16.90–∞) | 1.61 × 10−18 | NA (18.14–∞) | 7.70 × 10−19 |
| 22q11.2 dup^ | 2 (0.01/0.02) | 17 (0.07/0.12) | 0.15 (0.02–0.67) | 0.0043 | 0.18 (0.02–0.77) | 0.014 |
| NRXN1 del§ | 24 (0.16/0.22) | 5 (0.05/0.01) | 6.47 (2.42–21.71) | 1.34 × 10−5 | 6.48 (2.38–22.02) | 2.57 × 10−5 |
| PWS/AS dup§ | 11 (0.09/0.08) | 0 (0.00/0.00) | NA (3.38–∞) | 8.44 × 10−5 | NA (3.36–∞) | 8.49 × 10−5 |
| VIPR2 dup* | 12 (0.11/0.05) | 14 (0.07/0.09) | 1.15 (0.49–2.69) | 0.84 | 1.12 (0.46–2.67) | 0.84 |
| WBS dup§ | 6 (0.05/0.04) | 2 (0.00/0.02) | 4.04 (0.72–40.93) | 0.080 | 5.10 (0.94–51.62) | 0.037 |
Association between schizophrenia and CNVs at 15 specific risk loci and the protective 22q11.2 duplication locus. Association statistics are calculated with a Fisher’s Exact test (two-sided) and a Cochran-Mantel-Haenszel Exact test (two-sided) stratified by gender. SCZ = schizophrenia, PWS/AS = Prader-Willi/Angelman syndrome. WBS = Williams-Beuren syndrome.
§Risk locus (strong evidence).
*Risk locus (weaker evidence).
^Protective locus.