Table 2. CNVs in 11 Schizophrenia Risk Loci and the 22q11.2 Duplication Protective Locus in the New Data Set.
| CNV | Region (hg19) | CNVs, No. (%) | OR (95% CI) | P Valueb | |
|---|---|---|---|---|---|
| Controls (n = 8751) |
Casesa (n = 6934) |
||||
| 1q21.1 del | chr1:146,527,987-147,394,444 | 1 (0.011) | 11 (0.16) | 13.90 (2.02-596.86) | .0009 |
| 1q21.1 dup | chr1:146,527,987-147,394,444 | 4 (0.046) | 6 (0.087) | 1.89 (0.45-9.13) | .24 |
| NRXN1 exonic del | chr2:50,145,643-51,259,674 | 4 (0.046) | 5 (0.072) | 1.58 (0.34-7.96) | .36 |
| 3q29 del | chr3:195,720,167-197,354,826 | 1 (0.011) | 4 (0.058) | 5.05 (0.50-248.45) | .12 |
| WBS dup | chr7:72,744,915-74,142,892 | 0 | 1 (0.014) | Inf (0.032-Inf) | .44 |
| 15q11.2 del | chr15:22,805,313-23,094,530 | 24 (0.27) | 45 (0.65) | 2.38 (1.42-4.08) | .00034 |
| PWS/AS dup | chr15:22,805,313-28,390,339 | 0 | 6 (0.087) | Inf (1.49-Inf) | .0075 |
| 15q13.3 del | chr15:31,080,645-32,462,776 | 1 (0.011) | 3 (0.043) | 3.79 (0.30-198.64) | .23 |
| 16p13.11 dup | chr16:15,511,655-16,293,689 | 17 (0.19) | 32 (0.46) | 2.38 (1.28-4.58) | .0023 |
| 16p11.2 dup | chr16:29,650,840-30,200,773 | 3 (0.034) | 20 (0.29) | 8.43 (2.50-44.37) | 2.8 × 10−5 |
| 22q11.2 del | chr22:19,037,332-21,466,726 | 0 | 14 (0.20) | Inf (4.19-Inf) | 1.1 × 10−5 |
| 22q11.2 dup | chr22:19,037,332-21,466,726 | 4 (0.05) | 1 (0.01) | 0.32 (0.0064-3.19) | .27 |
Abbreviations: CNV, copy number variant; del, deletion; dup, duplication; Inf, infinity; OR, odds ratio; PWS/AS, Prader-Willi syndrome/Angelman syndrome; WBS, Williams-Beuren syndrome.
a
All results are in the expected direction of higher/lower rates in cases.
b
Fisher exact test (1-tailed).