Table 2.
| Table 2a. Known pathogenic CNVs associated with psychiatric disorders (deletions) | ||||||
|---|---|---|---|---|---|---|
| CNV Region a | Location (mb) | Freqcases | Freqcontrol | OR (CI) b | EMP-1sided c (adjusted) | EMP-2sided d (adjusted) |
| 1q21.1 * | chr1:145.0–148.0 | 5 | 1 | 6.27 (0.7–296.41) | 0.048 (0.29) | |
| 2p16.3 (NRXN1 exons) * | chr2:50.1–51.2 | 2 | 0 | 6.27 (0.24-Inf) | 0.19 (0.57) | |
| 3q29 * | chr3:195.7–197.3 | 6 | 0 | 16.32 (1.48-Inf) | 0.009 (0.022) | |
| 7q11.23 | chr7:72.7–74.1 | 0 | 0 | |||
| 7q36.3 (VIPR2) | chr7:158.8–158.9 | 0 | 0 | |||
| 15q11.2 | chr15:23.6–28.4 | 0 | 0 | |||
| 15q13.3 * | chr15:30.9–33.5 | 7 | 2 | 4.39 (0.84–43.34) | 0.05 (0.1) | |
| 16p13.11 | chr16:15.4–16.3 | 3 | 4 | 0.94 (0.14–5.56) | 1 (1) | 1 (1) |
| 16p11.2 distal * | chr16:28.2–29.0 | 2 | 1 | 2.51 (0.13–147.88) | 0.43 (0.80) | |
| 16p11.2 | chr16:29.5–30.2 | 0 | 0 | |||
| 17q12 * | chr17:34.8–36.2 | 0 | 0 | |||
| 22q11.2 * | chr22:18.7–21.8 | 6 | 0 | 16.32 (1.48-Inf) | 0.0037 (0.022) | |
| Table 2b. Known pathogenic CNVs associated with psychiatric disorders (duplications) | ||||||
|---|---|---|---|---|---|---|
| CNV Region a | Location (mb) | Freqcases | Freqcontrol | OR (CI) b | EMP-1sided c (adjusted) | EMP-2sided d (adjusted) |
| 1q21.1 | chr1:145.0–148.0 | 2 | 1 | 2.51 (0.13–147.88) | 0.36 (0.98) | |
| 2p16.3 (NRXN1) | chr2:50.1–51.2 | 0 | 0 | |||
| 3q29 | chr3:195.7–197.3 | 1 | 0 | 3.76 (0.03-Inf) | 0.40 (0.88) | |
| 7q11.23 | chr7:72.7–74.1 | 2 | 0 | 6.27 (0.24-Inf) | 0.24 (0.57) | |
| 7q36.3 (VIPR2) * | chr7:158.8–158.9 | 0 | 2 | 0.25 (0–6.68) | 1 (1) | 1 (1) |
| 15q11.2 | chr15:23.6–28.4 | 0 | 0 | |||
| 15q13.3 | chr15:30.9–33.5 | 1 | 2 | 0.63 (0.01–12.05) | 1 (1) | 1 (1) |
| 16p13.11 | chr16:15.4–16.3 | 12 | 6 | 2.51 (0.87–8.16) | 0.168 (0.713) | |
| 16p11.2 distal | chr16:28.2–29.0 | 2 | 4 | 0.63 (0.06–4.38) | 1 (1) | 0.68 (1) |
| 16p11.2 * | chr16:29.5–30.2 | 10 | 2 | 6.28 (1.34–59) | 0.0031 (0.022) | |
| 17q12 | chr17:34.8–36.2 | 5 | 1 | 6.27 (0.7–296.41) | 0.074 (0.318) | |
| 22q11.2 | chr22:18.7–21.8 | 0 | 3 | 0.18 (0–3.03) | 1 (1) | 0.26 (0.83) |
For NRXN1 in Table (2a), we considered all >100kb deletions disrupting exons (≥1bp overlap). For VIPR2 and NRXN1 in Table (2b), we considered all >100Kb CNV events that disrupted the gene (≥1bp overlap). For all other regions, we considered all >100kb CNV events that had >50% reciprocal overlap with a region (PLINK --cnv-union-overlap 0.5).
When 0 events occurred, ORs were estimated by applying the standard continuity correction that added a value of 0.5 to each cell of the 2x2 table.
Test was one-sided assuming higher rate in cases and statistical significance was estimated empirically by 100,000 permutations within batches. The multiple-testing-adjusted P value was obtained in PLINK using the default max-T method.
For simplicity, results for 2-sided tests were only shown when Freqcotnrol > Freqcase.
The star indicates previously implicated loci in SCZ.