Table 3. Validated CNVs discovered using affected children from Utah families.
| TaqMan validated Utah and sequence SNP CNV regions of significance | |||||||||||
| CNV Origin | Cytoband | CNV Region - Discovery Cohort | CNV Region - Replication Cohort | CNV Type | Total Cases | Total Controls | OddsRatio | P Value | Cases | Controls | Gene/Region |
| Utah CNV | 1q21.1 | chr1:145714421-146101228 | chr1:145703115-145736438 | Dup | 1542 | 5754 | 3.37 | 9.60E-03 | 9 | 10 | CD160, PDZK1 |
| Utah CNV | 1q41 | chr1:215858193-215861879 | chr1:215854466-215861792 | Del | 1540 | 5754 | 2.12 | 5.02E-03 | 22 | 39 | USH2A |
| Utah CNV | 2p16.3 | chr2:51272055-51336043 | chr2:51266798-51339236 | Del | 1542 | 5755 | 14.96 | 8.26E-03 | 4 | 1 | upstream of NRXN1 |
| Utah CNV# | 3q26.31 | chr3:172596081-172617355 | chr3:172591359-172604675 | Dup | 1540 | 5754 | 3.74 | 2.11E-01 | 1 | 1 | downstream of SPATA16 |
| Utah CNV# | 4q35.2 | chr4:189084983-189117429 | chr4:189084240-189117031 | Del | 1544 | 5762 | 3.74 | 1.98E-01 | 2 | 2 | downstream of TRIML1 |
| Utah CNV# | 6p24.3 | chr6:7425246-7464367 | chr6:7461346-7470321 | Del | 1544 | 5762 | ∞ | 2.11E-01 | 1 | 0 | between RIOK1 and DSP |
| Utah CNV# | 6q11.1 | chr6:62443739-62462295 | chr6:62426827-62472074 | Dup | 1544 | 5762 | 3.74 | 1.98E-01 | 2 | 2 | KHDRBS2 |
| Utah CNV | 6q24.3 | chr6:147588752-147664671 | chr6:147577803-147684318 | Del | 1533 | 5751 | ∞ | 2.10E-01 | 1 | 0 | STXBP5 |
| Utah CNV# | 7p22.1 | chr7:6838712-6864071 | chr7:6870635-6871412 | Dup | 1544 | 5762 | 7.47 | 1.15E-01 | 2 | 1 | upstream of CCZ1B |
| Sequence SNP CNV# | 7q21.3 | Not found | chr7:93070811-93116320 | Del | 1544 | 5762 | ∞ | 4.46E-02 | 2 | 0 | CALCR, MIR653, MIR489 |
| Utah CNV# | 9p21.1 | chr9:28190069-28347679 | chr9:28207468-28348133 | Del | 1544 | 5761 | 3.74 | 6.72E-02 | 4 | 4 | LINGO2 |
| Utah CNV# | 9p21.1 | chr9:28190069-28347679 | chr9:28354180-28354967 | Del | 1544 | 5762 | 3.73 | 3.78E-01 | 1 | 1 | LINGO2 (intron) |
| Utah CNV | 10q23.1 | chr10:83893626-84175018 | chr10:83886963-83888343 | Del | 1505 | 5640 | 3.76 | 1.54E-02 | 7 | 7 | NRG3 (intron) |
| Utah CNV# | 10q23.31 | chr10:92274764-92289762 | chr10:92262627-92298079 | Dup | 1544 | 5761 | 7.47 | 1.15E-01 | 2 | 1 | downstream of BC037970 |
| Utah CNV# | 12q23.2 | chr12:102097012-102106306 | chr12:102095178-102108946 | Dup | 1544 | 5762 | 7.47 | 1.15E-01 | 2 | 1 | CHPT1 |
| Utah CNV# | 13q13.3 | chr13:40087689-40088007 | chr13:40089105-40090197 | Del | 1544 | 5761 | ∞ | 2.11E-01 | 1 | 0 | LHFP (intron) |
| Sequence SNP CNV# | 14q32.2 | Not found | chr14:100705631-100828134 | Dup | 1544 | 5762 | 9.36 | 5.99E-03 | 5 | 2 | SLC25A29, YY1, MIR345, SLC25A47, WARS |
| Sequence SNP CNV# | 14q32.31 | Not found | chr14:102018946-102026138 | Dup | 1544 | 5762 | 4.62 | 1.01E-14 | 60 | 50 | DIO3AS, DIO3OS |
| Sequence SNP CNV# | 14q32.31 | Not found | chr14:102729881-102749930 | Del | 1544 | 5762 | 7.47 | 1.15E-01 | 2 | 1 | MOK |
| Sequence SNP CNV# | 14q32.31 | Not found | chr14:102973910-102975572 | Dup | 1544 | 5762 | 3.82 | 8.29E-26 | 136 | 142 | ANKRD9 (RAGE) |
| Sequence SNP CNV | 15q11.2-q13.1 | Not found | chr15:25690465-28513763 | Dup* | 1544 | 5762 | 41.05 | 1.82E-08 | 11 | 1 | ATP10A, GABRB3, GABRA5, GABRG3, HERC2 |
| Sequence SNP CNV# | 15q13.2–15q13.3 | Not found | chr15:31092983-31369123 | Del | 1543 | 5761 | ∞ | 4.46E-02 | 2 | 0 | FAN1, MTMR10, MIR211, TRPM1 |
| Sequence SNP CNV# | 15q13.3 | Not found | chr15:31776648-31822910 | Dup | 1544 | 5762 | 4.40 | 6.91E-06 | 21 | 18 | OTUD7A |
| Sequence SNP CNV# | 20q11.22 | Not found | chr20:32210931-32441302 | Dup | 1544 | 5762 | 2.72 | 3.16E-02 | 8 | 11 | NECAB3, CBFA2T2, C20orf144, NECAB3, C20orf134, PXMP4, NECAB3, ZNF341, E2F1, CHMP4B |
CNVs shown here were selected based on their p value, their case/control odds ratio, or both and were subject to molecular validation.
*
This CNV is contiguous with the chromosome 15q11.2 CNV described in Table 4 based on TaqMan data.
#
Designates CNVs not previously seen in ASD, based on queries for genes included in or flanking the CNV.