Rare Genome-Wide Copy Number Variation and Expression of Schizophrenia in 22q11.2 Deletion Syndrome
Abstract
Objective:
Method:
Results:
Conclusions:
Method
Ascertainment of Samples From 22q11.2DS Subjects for CNV Data
Phenotype and Diagnostic Group Determination
CNV Detection and Annotation
CNV Burden Analysis and Statistical Approach
Gene Set Enrichment Analysis
Network Connectivity Test and Network Construction
Results
22q11.2 Deletions
Quantitative Genome-Wide Burden of Additional Rare CNVs
Variable | 22q11.2DS-Schizophrenia (N=142)a | 22q11.2DS-Nonpsychotic (N=149)a | Analysis | |||
---|---|---|---|---|---|---|
Median | Range | Median | Range | z | p | |
Deletion or duplication | 2 | 1–26 | 2 | 1–26 | 1.5787 | 0.1144 |
Deletionb | 2 | 1–18 | 1 | 1–14 | 2.7569 | 0.0058 |
Duplication | 2 | 1–26 | 2 | 1–26 | 0.1470 | 0.8831 |
Functional Burden of Additional Rare CNVs
22q11.2DS-Schizophrenia (N=142)b | 22q11.2DS-Nonpsychotic (N=149)b | Analyses | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Gene Set Name | Total Genes (N) | CNVs (N) | Subjects | CNVs (N) | Subjects | p | FDR-BH | Odds Ratio | ||
N | % | N | % | |||||||
Nervous system phenotype (MGI) | 2,609 | 37 | 32 | 22.5 | 16 | 15 | 10.1 | 0.00062 | 0.012 | 2.36 |
Neurobehavioral phenotype (MGI) | 2,602 | 37 | 33 | 23.2 | 19 | 19 | 12.8 | 0.00174 | 0.016 | 2.21 |
Neural phenotype union (MGI) | 3,764 | 48 | 42 | 29.6 | 25 | 24 | 16.1 | 0.00260 | 0.016 | 1.80 |
Muscle/cardiovascular phenotype (MGI) | 2,327 | 27 | 25 | 17.6 | 13 | 13 | 8.7 | 0.00481 | 0.022 | 2.38 |
Endocrine/exocrine/reproduction phenotype (MGI) | 2,298 | 31 | 31 | 21.8 | 18 | 17 | 11.4 | 0.01099 | 0.042 | 2.08 |
Synaptic (Gene Ontology) | 860 | 15 | 14 | 9.9 | 6 | 6 | 4.0 | 0.02472 | 0.078 | 2.81 |
CNV | Subject | Chromosome | Cytoband | Startb | Size | Genes (N) | Very Rare CNVc | Flanking Low-Copy Repeats | All Genes Overlapped by CNV | Gene(s) Contributing to Nervous System Gene Set Results |
---|---|---|---|---|---|---|---|---|---|---|
1 | 17 | 1 | 1p22.1 | 94463617 | 18760 | 1 | • | ABCA4 | ABCA4 | |
2 | 130 | 1 | 1q32.2 | 209881045 | 28340 | 1 | • | HSD11B1 | HSD11B1 | |
3 | 93 | 1 | 1q43 | 237492310 | 26855 | 1 | • | RYR2 | RYR2 | |
4 | 144 | 2 | 2q35 | 216834680 | 340811 | 5 | • | TMEM169, MARCH4, PECR, XRCC5, MREG | XRCC5 | |
5 | 39 | 3 | 3p26.1 | 7619772 | 536651 | 1 | • | GRM7 | GRM7 | |
6 | 55 | 3 | 3p22.2 | 38608585 | 510439 | 4 | • | WDR48, SCN11A, SCN5A, SCN10A | SCN11A, SCN5A, SCN10A | |
7 | 28 | 3 | 3q29 | 195263161 | 232072 | 4 | APOD, MUC4, MUC20, PPP1R2, miR–570–5p, miR–570–3p | APOD | ||
8 | 130 | 4 | 4p16.3 | 3463452 | 10187 | 1 | • | DOK7 | DOK7 | |
9 | 42 | 4 | 4p15.2 | 26433603 | 49693 | 2 | • | RBPJ, CCKAR | CCKAR | |
10 | 65 | 4 | 4q35.1 | 186979699 | 76584 | 1 | TLR3 | TLR3 | ||
11 | 110 | 6 | 6q11.1 | 62234532 | 270027 | 2 | MTRNR2L9, KHDRBS2 | KHDRBS2 | ||
12 | 15 | 6 | 6q26 | 161687430 | 1202784 | 2 | • | AGPAT4, PARK2 | PARK2 | |
13 | 150 | 6 | 6q27 | 168167050 | 228482 | 2 | • | MLLT4, HGC6.3 | MLLT4 | |
14 | 141 | 7 | 7p21.2 | 13946099 | 33357 | 1 | • | ETV1 | ETV1 | |
15 | 55 | 7 | 7q21.11 | 81993260 | 185718 | 1 | CACNA2D1 | CACNA2D1 | ||
16 | 114 | 8 | 8p23.3 | 427857 | 77504 | 1 | • | TDRP | TDRP | |
17 | 127 | 8 | 8p22 | 13329776 | 290648 | 2 | • | DLC1, C8orf48 | DLC1 | |
18 | 110 | 8 | 8p12 | 34906448 | 250455 | 1 | • | UNC5D | UNC5D | |
19d | 143 | 8 | 8q12.1 | 56722133 | 159268 | 2 | LYN, TGS1 | LYN | ||
20 | 79 | 9 | 9q22.2 | 93616404 | 82699 | 1 | SYK | SYK | ||
21 | 10 | 10 | 10q23.31 | 89651696 | 46930 | 1 | • | PTEN | PTEN | |
22 | 35 | 10 | 10q24.2 | 99411165 | 39708 | 2 | AVPI1, PI4K2A | PI4K2A | ||
23 | 15 | 11 | 11q13.5 | 76735763 | 156340 | 4 | • | B3GNT6, OMP, MYO7A, CAPN5 | MYO7A, OMP | |
24 | 86 | 11 | 11q23.3 | 115010867 | 139977 | 1 | • | CADM1 | CADM1 | |
25 | 12 | 12 | 12q24.21, 12q24.22 | 116396113 | 1021914 | 6 | • | FBXW8, MAP1LC3B2, MED13L, RNFT2, C12orf49, HRK, miR–4472, miR–620 | FBXW8 | |
26 | 116 | 13 | 13q12.12 | 23397621 | 1690189 | 9 | • | SPATA13, C1QTNF9, C1QTNF9B, SGCG, C1Q, TNF9B-AS1, PARP4, MIPEP, SACS, TNFRSF19, miR–2276–5p, miR–2276–3p | C1QTNF9B, TNFRSF19 | |
27 | 30 | 14 | 14q32.11 | 91288380 | 77382 | 1 | • | RPS6KA5 | RPS6KA5 | |
28e | 92 | 15 | 15q13.2,15q13.3 | 30668479 | 1952748 | 9 | • | KLF13, OTUD7A, MTMR10, FAN1, CHRNA7, LOC283710, ARHGAP11B, TRPM1, CHRFAM7A, miR–211–5p, miR–211–3p | CHRNA7, TRPM1 | |
29e | 52 | 15 | 15q13.2,15q13.3 | 30747394 | 2129590 | 9 | • | KLF13, OTUD7A, MTMR10, FAN1, GOLGA8O, CHRNA7, LOC283710, ARHGAP11B, TRPM1, miR–211–5p, miR–211–3p | CHRNA7, TRPM1 | |
30 | 131 | 15 | 15q25.1 | 78421669 | 15345 | 1 | • | CIB2 | CIB2 | |
31 | 33 | 16 | 16q24.3 | 89420230 | 258822 | 4 | • | RPL13, SPG7, CPNE7, ANKRD11 | SPG7 | |
32d,e | 132 | 17 | 17q12 | 34816256 | 1428102 | 15 | • | ZNHIT3, LHX1, DUSP14, MRM1, ACACA, DDX52, DHRS11, SYNRG, C17orf78, HNF1B, AATF, MYO19, PIGW, TADA2A, GGNBP2, miR–378j, miR–2909 | LHX1 | |
33 | 147 | 18 | 18q23 | 74711326 | 80540 | 1 | • | MBP | MBP | |
34 | 34 | 20 | 20p13 | 4895803 | 181274 | 1 | • | SLC23A2 | SLC23A2 | |
35 | 130 | 20 | 20p11.21 | 25061344 | 198784 | 3 | • | ENTPD6, PYGB, VSX1 | VSX1 | |
36 | 41 | 21 | 21q22.2 | 41337036 | 120608 | 1 | • | DSCAM | DSCAM | |
37 | 121 | 22 | 22q11.23 | 23675258 | 1384582 | 26 | • | SMARCB1, MMP11, C22orf43, DDTL, RGL4, SLC2A11, MIF, CHCHD10, DERL3, C22orf15, IGLL1, GSTT2B, ZNF70, DDT, VPREB3, GSTT2, ADORA2A, SNRPD3, FAM211B, CABIN1, SPECC1L, GUCD1, SUSD2, GGT5, UPB1, GGT1 | ADORA2A, MIF, SMARCB1 |
Potential Mechanisms of Rare CNV-Related Risk for Schizophrenia in 22q11.2DS
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