Table 2.
List of reported and unreported CNVs with candidate genes identified in the patients and controls in the present study and their frequencies in other populations.
| Reported CNVs | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| CNV (coordinate) | Present study | Published reports | |||||||||
| No. of patients | No. of controls | Odds ratio (CI interval) | p-value | Patients | Controls | Odds ratio (CI interval) | p-value | ||||
| With CNV | Total | With CNV | Total | Study group | |||||||
| 6p21.33 del (chr6:31360255–31453618) | 1 | 1 | 1.00 (0.06–16.1) | 1.00 | 6 | 8,290 | 4 | 7,431 | 1.34 (0.38–4.77) | 0.64 | American |
| 8p23.2 del (chr8:3681516–3832465) | 2 | 1 | 2.01 (0.18–22.4) | 0.57 | 6 | 8,290 | 2 | 7,431 | 2.69 (0.54–13.3) | 0.2256 | American |
| 11q14.1 del (chr11:83930211–84642163) | 1 | 0 | 3.01 (0.12–74.6) | 0.49 | 3 | 1,699 | 0 | 824 | 3.40 (0.17–65.9) | 0.42 | Chinese and Japanese |
| 14q21.1 del (chr14:41855338–43171423) | 1 | 0 | 3.01 (0.12–74.6) | 0.49 | NA | NA | NA | NA | NA | NA | Family studies |
| 15q11.2 del (chr15:22755185–23236972) | 2 | 0 | 5.06 (0.24–106.2) | 0.29 | 44 | 6,882 | 47 | 11,255 | 1.53 (1.01–2.32) | 0.04 | Multiple populations |
| 6 | 307 | 3 | 359 | 2.37 (0.59–9.53) | 0.23 | South Indian | |||||
| 20p12.1 del (chr20:14890211–15122254) | 1 | 0 | 3.01 (0.12–74.6) | 0.49 | 1 | 454 | 0 | 416 | 2.75 (0.11–67.67) | 0.54 | Canadian |
| 22q11.21 del (chr22:19195680–20267213) | 1 | 0 | 3.01 (0.12–74.6) | 0.49 | 64 | 21,094 | 1 | 20,227 | 88.9 (12.34–641) | <0.0001 | European, Asian, African American |
| 4q13.2-q13.3 dup (chr4:69697128–71389594) | 1 | 0 | 3.01 (0.12–74.6) | 0.49 | 1 | 3,518 | 0 | 4,328 | 3.61 (0.15–88.7) | 0.43 | European |
| 7q36.2 dup (chr7:153154107–153652188) | 1 | 0 | 3.01 (0.12–74.6) | 0.49 | 7 | 8,290 | 3 | 7,431 | 2.09 (0.54–8.1) | 0.28 | American |
| 7q21.11 dup (chr7:83179622–83437224) | 0 | 1 | 0.33 (0.01–8.19) | 0.49 | 1 | 1,699 | 0 | 824 | 1.46 (0.06–35.79) | 0.81 | Chinese and Japanese |
| 15q11.2 dup (chr15:22755185–23236972) | 1 | 1 | 1.00 (0.06–16.1) | 1.00 | 23 | 8,290 | 16 | 7,431 | 1.29 (0.68–2.44) | 0.43 | American |
| 16p13.11 dup (chr16:15548310–16291983) | 0 | 1 | 0.33 (0.01–8.19) | 0.49 | 37 | 12,029 | 93 | 69,289 | 2.3 (1.57–3.36) | <0.0001 | Multiple populations |
| 22q11.22 dup (chr22:22316631–22555078) | 5 | 2 | 2.55 (0.48–13.3) | 0.26 | NA | NA | NA | NA | NA | NA | Family studies |
| Unreported CNVs with candidate genes | ||||||||
|---|---|---|---|---|---|---|---|---|
| CNVs with Odds ratio-3.01; CI-0.12-74.61 and p value 0.49 | ||||||||
| CNV | Coordinate | No. of patients | No. of controls | Candidate gene | GWAS | Exome | Transcriptome and eQTL | Differential methylation and meQTL |
| 2q32.1-q32.2 del | (chr2:186067813–190115961) | 1 | 0 | CALCRL | *** | NA | *** | *** |
| COL3A1 | * | PD | *** | *** | ||||
| DIRC1 | *** | PD | NA | NA | ||||
| ITGAV | * | D | *** | *** | ||||
| ZSWIM2 | * | PD | *** | *** | ||||
| 11p15.3 del | (chr11:10970735–11294339) | 1 | 0 | GALNT18 | NA | NA | *** | *** |
| 1q42.13 dup | (chr1:228467711–228564884) | 1 | 0 | OBSCN | – | PD | *** | *** |
| 2p22.3 Dup | (chr2:32713706–33152042) | 1 | 0 | BIRC6 | ** | PD | *** | *** |
| 7p11.2 Dup | (chr7:55804513–56294281) | 1 | 0 | CCT6A | * | B | NS | *** |
| 7q21.3 Dup | (chr7:96567080–97107457) | 1 | 0 | DLX5 | *** | NA | *** | *** |
| 9p22.1 Dup | (chr9:18882562–19192694) | 1 | 0 | ADAMTSL1 | *** | B | *** | *** |
| 13q12.3-q13.1 Dup | (chr13:32175095–32525678) | 1 | 0 | EEF1DP3 | * | NA | NS | *** |
| CNVs with Odds ratio-5.06; CI-0.24-106.20 and p value 0.29 | ||||||||
| 16p13.3 del | (chr16:538565–863498) | 2 | 0 | CAPN15 | PD | *** | *** | |
| 3p14.2 Dup | (chr3:62611243–63258941) | 2 | 0 | CADPS | *** | NA | NS | *** |
| CNVs with Odds ratio-1.00; CI-0.06-16.12 and p value 1.00 | ||||||||
| 16p13.3 del | (chr16:6837553–6960281) | 1 | 1 | RBFOX1 | *** | NA | *** | *** |
| 11p15.4 Dup | (chr11:9645397–10143942) | 1 | 1 | SBF2 | *** | NA | *** | *** |
| 11q22.3 Dup | (chr11:106956255–107426129) | 1 | 1 | CWF19L2 | *** | PD | *** | *** |
| 16p13.3 Dup | (chr16:6546624–6672741) | 1 | 1 | Same as in deletion | ||||
| CNVs with Odds ratio-0.17; CI-0.03-0.78 and p value 0.02 | ||||||||
| 4q35.1-q35.2 Dup | (chr4:186935500–187122319) | 2 | 11 | FAM149A | *** | NA | *** | *** |
| TLR3 | * | B | NS | *** | ||||
| CNVs with Odds ratio-0.24; CI-0.02-2.22 and p value 0.21 | ||||||||
| 7q11.23 Dup | (chr7: 76131646–76637441) | 1 | 4 | DTX2 | ** | PD | *** | *** |
| POMZP3 | ** | D | *** | *** | ||||
| CNVs with Odds ratio-1.50; CI-0.24-9.14 and p value 0.65 | ||||||||
| 19p13.3 Dup | (chr19:789890–1397443) | 3 | 2 | Same as in deletion | ||||
Unreported CNVs do not have population-level data. NA, No data available; NS, Not significant; D, Damaging mutation; PD, Probably damaging mutation; B, Benign; ‘–’ p value close to 0.05, *p value 0.05–0.02, **p value 0.02–0.01, ***p value <0.001.