Prenatal Expression Patterns of Genes Associated With Neuropsychiatric Disorders
Abstract
Objective
Method
Results
Conclusions
Method
Gene Set Assignment
Statistical Methods
Results
Fetal Effect Analysis
Gene Set | N of Genes | N of Genes Mapped to a Probe | % of Genes in Gene Set with Fetal Effect >0 | p | % of Genes in Gene Set with Fetal Effect >0.5 | p (Two-Sided) | % of Genes in Gene Set with Fetal Effect >1 | p | % of Genes in Gene Set with Fetal Effect >1.5 | p |
---|---|---|---|---|---|---|---|---|---|---|
Genome-wide | 17,678 | 43 | 25 | 12 | 5 | |||||
Neurodevelopmental disorders | 33 | 31 | 65 | 1.13E−02 | 52 | 3.37E−03 | 23 | 1.50E−01 | 16 | 9.64E−02 |
Schizophrenia (SRF) Meta-analysis | 40 | 36 | 42 | 8.95E−01 | 22 | 6.57E−01 | 8 | 4.57E−01 | 3 | 3.87E−01 |
Schizophrenia (PGC) GWAS | 132 | 106 | 50 | 1.13E−01 | 29 | 4.58E−01 | 15 | 3.21E−01 | 6 | 8.02E−01 |
Schizophrenia CNV | 154 | 113 | 41 | 6.58E−01 | 26 | 9.29E−01 | 11 | 6.94E−01 | 4 | 7.09E−01 |
Schizophrenia SNV/INDEL | 240 | 212 | 48 | 1.54E−01 | 29 | 2.06E−01 | 15 | 1.75E−01 | 6 | 7.47E−01 |
ASD CNV | 216 | 176 | 41 | 5.57E−01 | 23 | 5.60E−01 | 9 | 2.30E−01 | 3 | 2.11E−01 |
ASD database | 262 | 242 | 49 | 4.58E−02 | 36 | 3.45E−04 | 19 | 4.06E−03 | 11 | 2.98E−03 |
Bipolar disorder GWAS | 146 | 123 | 38 | 3.00E−01 | 24 | 8.15E−01 | 11 | 8.95E−01 | 6 | 7.95E−01 |
Intellectual disability | 94 | 88 | 56 | 1.46E−02 | 40 | 5.53E−03 | 22 | 2.50E−02 | 13 | 3.70E−02 |
Neurodegenerative disorders | 59 | 46 | 28 | 2.90E−02 | 11 | 1.67E−03 | 4 | 1.37E−02 | 0 | |
Overlap across all categories | 62 | 45 | 7.03E−01 | 31 | 3.61E−01 | 16 | 3.50E−01 | 11 | 1.26E−01 | |
Schizophrenia/ASD CNV overlap | 73 | 45 | 6.74E−01 | 26 | 8.87E−01 | 8 | 2.71E−01 | 4 | 6.55E−01 |
Functional Analysis of Prenatally Enriched Genes
Secondary Analysis of CNV Regions
CNV Loci Associated With ASD and Schizophrenia | ||||
---|---|---|---|---|
Locus | CNV Type | Gene | Fetal Effect | p |
1q21.1 | Dup/Del | NBPF13P | n/a | |
PRKAB2 | 1.39 | 8.97E−57 | ||
FMO5 | ||||
CHD1L | n/a | |||
BCL9 | 2.02 | 2.50E−63 | ||
ACP6 | n/a | |||
GJA5 | 0.25 | 2.82E−03 | ||
GJA8 | −0.49 | 1.40E−09 | ||
GPR89B | n/a | |||
GPR89C | n/a | |||
PDZK1P1 | n/a | |||
NBPF8 | n/a | |||
NBPF24 | n/a | |||
NBPF11 | n/a | |||
NBPF10 | n/a | |||
2p16.3 | Dup/Del | NRXN1 | 1.31 | 6.02E−34 |
15q13.3 | Del/Dup | CHRFAM7A | −1.54 | 5.29E−32 |
ARHGAP11B | n/a | |||
MTMR15 | 0.50 | 1.10E−12 | ||
MTMR10 | n/a | |||
TRPM1 | n/a | |||
MIR211 | n/a | |||
KLF13 | −0.53 | 2.04E−09 | ||
OTUD7A | −0.96 | 6.01E−21 | ||
| | CHRNA7 | 0.83 | 4.76E−08 |
16p11.2 | Del/Dup | SPN | 0.15 | 7.88E−04 |
QPRT | −0.86 | 3.41E−22 | ||
C16orf54 | −0.01 | 9.09E−01 | ||
ZG16 | n/a | |||
KIF22 | 0.22 | 4.67E−04 | ||
MAZ | −0.06 | 7.63E−02 | ||
PRRT2 | −0.57 | 3.02E−13 | ||
PAGR1 (C16orf53) | 1.29 | 1.49E−51 | ||
MVP | −1.16 | 3.84E−28 | ||
CDIPT | −0.59 | 9.04E−32 | ||
SEZ6L2 | −1.44 | 1.83E−42 | ||
ASPHD1 | 0.74 | 1.69E−15 | ||
KCTD13 | 0.16 | 1.68E−02 | ||
TMEM219 | −0.95 | 1.04E−47 | ||
TAOK2 | 0.50 | 7.67E−07 | ||
HIRIP3 | 0.16 | 2.33E−02 | ||
INO80E | −0.03 | 4.98E−01 | ||
DOC2A | −0.64 | 3.67E−30 | ||
C16orf92 | n/a | |||
FAM57B | −0.64 | 3.67E−30 | ||
ALDOA | 0.32 | 1.08E−06 | ||
PPP4C | 1.29 | 1.69E−49 | ||
TBX6 | −0.78 | 1.59E−18 | ||
YPEL3 | −0.95 | 1.35E−39 | ||
GDPD3 | 0.24 | 2.03E−05 | ||
MAPK3 | −1.22 | 2.91E−55 | ||
| | CORO1A | −0.97 | 5.34E−40 |
22q11.21 | Del/Dup | DGCR6 | −0.73 | 2.53E−31 |
PRODH | −1.01 | 6.36E−17 | ||
DGCR5 | 0.65 | 4.41E−13 | ||
DGCR9 | -0.60 | 3.13E−10 | ||
DGCR10 | 0.56 | 3.37E−05 | ||
DGCR2 | −0.73 | 2.09E−28 | ||
DGCR11 | 0.00 | 9.72E−01 | ||
DGCR14 | 0.45 | 1.60E−07 | ||
TSSK2 | −0.55 | 9.14E−08 | ||
GSC2 | n/a | |||
SLC25A1 | 0.48 | 2.19E−15 | ||
CLTCL1 | 0.48 | 2.19E−15 | ||
HIRA | 0.58 | 9.08E−24 | ||
MRPL40 | −0.50 | 1.74E−13 | ||
C22orf39 | n/a | |||
UFD1L | 0.25 | 5.60E−07 | ||
CDC45L | 3.89 | 1.59E−68 | ||
CLDN5 | n/a | |||
SEPT5 | ||||
GP1BB | n/a | |||
TBX1 | −0.70 | 6.57E−25 | ||
GNB1L | -0.25 | 1.14E−04 | ||
C22orf29 | 0.07 | 1.70E−01 | ||
TXNRD2 | −0.84 | 9.34E−41 | ||
COMT | −0.28 | 2.66E−07 | ||
ARVCF | 0.57 | 4.53E−21 | ||
C22orf25 | −1.47 | 8.40E−63 | ||
MIR185 | n/a | |||
DGCR8 | 0.82 | 1.92E−09 | ||
MIR3618 | n/a | |||
MIR1306 | n/a | |||
TRMT2A | −0.40 | 1.14E−08 | ||
RANBP1 | 0.40 | 4.51E−16 | ||
ZDHHC8 | −0.16 | 4.09E−04 | ||
RTN4R | −0.81 | 5.47E−18 | ||
MIR1286 | n/a | |||
DGCR6L | −0.74 | 4.76E−32 | ||
TMEM191B | n/a | |||
RIMBP3 | n/a | |||
ZNF74 | 1.57 | 2.05E−62 | ||
SCARF2 | −0.17 | 2.92E−03 | ||
KLHL22 | 0.38 | 5.11E−16 | ||
MED15 | −0.49 | 1.36E−21 | ||
PI4KA | 0.50 | 2.81E−08 | ||
SERPIND1 | 0.74 | 2.23E−09 | ||
SNAP29 | −0.69 | 6.90E−19 | ||
CRKL | 0.05 | 3.49E−01 | ||
AIFM3 | n/a | |||
LZTR1 | 0.56 | 1.98E−22 | ||
THAP7 | −0.13 | 7.74E−04 | ||
P2RX6 | 0.16 | 2.00E−03 | ||
SLC7A4 | −0.83 | 1.97E−26 | ||
HIC2 | 2.32 | 1.97E−26 |
Locus | CNV Type | Genes | Fetal Effect | p |
---|---|---|---|---|
1q21.1 | Del | HFE2 | 0.09 | 4.82E−01 |
TXNIP | 0.86 | 2.33E−09 | ||
POLR3GL | 0.05 | 2.97E−01 | ||
ANKRD34A | −0.98 | 5.24E−33 | ||
LIX1L | 1.38 | 6.15E−59 | ||
RBM8A | 0.90 | 2.48E−37 | ||
GNRHR2 | −0.49 | 3.85E−07 | ||
PEX11B | −0.70 | 1.44E−36 | ||
ITGA10 | n/a | |||
ANKRD35 | −0.61 | 2.04E−14 | ||
PIAS3 | 0.07 | 1.46E−01 | ||
NUDT17 | −0.30 | 3.23E−08 | ||
POLR3C | 0.19 | 6.81E−05 | ||
RNF115 | 0.08 | 2.06E−01 | ||
CD160 | −0.49 | 1.18E−15 | ||
PDZK1 | 0.23 | 3.52E−02 | ||
GPR89A | n/a |
Locus | CNV Type | Gene | Fetal Effect | p |
---|---|---|---|---|
3p14.1 | Del | SUCLG2 | −0.60 | 1.49E−16 |
FAM19A1 | n/a | |||
FAM19A4 | n/a | |||
C3orf64 | ||||
MIR3136 | n/a | |||
TMF1 | 0.24 | 1.03E−01 | ||
UBA3 | 1.38 | 2.01E−56 | ||
ARL6IP5 | −1.02 | 4.03E−40 | ||
LMOD3 | -0.35 | 6.50E−03 | ||
FRMD4B | 1.78 | 1.97E−34 | ||
| | MITF | 0.17 | 3.79E−02 |
7q11.23 | Dup | FZD9 | −0.41 | 3.34E−05 |
BAZ1B | 0.15 | 9.52E−03 | ||
BCL7B | 0.21 | 1.84E−03 | ||
TBL2 | 0.17 | 9.66E−03 | ||
MLXIPL | n/a | |||
VPS37D | 0.81 | 8.78E−26 | ||
DNAJC30 | 0.20 | 5.41E−04 | ||
WBSCR22 | −0.37 | 2.77E−14 | ||
STX1A | −1.52 | 5.20E−49 | ||
MIR4284 | n/a | |||
ABHD11 | 0.04 | 6.41E−01 | ||
CLDN3 | −0.27 | 3.53E−06 | ||
CLDN4 | 0.02 | 8.86E−01 | ||
WBSCR27 | −0.29 | 2.74E−02 | ||
WBSCR28 | 0.19 | 1.21E−02 | ||
ELN | −0.03 | 7.20E−01 | ||
LIMK1 | −0.50 | 2.58E−10 | ||
MIR590 | n/a | |||
LAT2 | −1.22 | 5.75E−15 | ||
RFC2 | 0.83 | 3.10E−39 | ||
CLIP2 | 0.18 | 7.63E−03 | ||
GTF2IRD1 | 1.68 | 1.64E−68 | ||
| | GTF2I | n/a | |
7q31.1 | Del/Dup | DOCK4 | 0.12 | 1.67E−01 |
8p23.3 | Dup | DLGAP2 | −2.22 | 1.96E−66 |
9p24.3 | Del/Dup | FOXD4 | n/a | |
CBWD1 | 0.52 | 2.04E−13 | ||
C9orf66 | −0.38 | 2.01E−07 | ||
| | DOCK8 | −1.52 | 4.19E−18 |
10q11.23-21.1 | Dup | PRKG1 | n/a | |
MIR605 | n/a | |||
CSTF2T | 0.39 | 1.29E−06 | ||
DKK1 | 0.01 | 9.12E−01 | ||
| | MBL2 | 0.23 | 2.37E−02 |
12q24.31 | Dup | TMEM120B | n/a | |
RHOF | −1.58 | 1.67E−63 | ||
SETD1B | 1.30 | 6.47E−58 | ||
HPD | −0.12 | 9.20E−02 | ||
PSMD9 | 0.18 | 1.09E−02 | ||
WDR66 | −0.58 | 5.32E−10 |
Secondary Analysis of Genes in the ASD Database
Secondary Analysis of Genes Associated With Schizophrenia by Exome Sequencing of Rare Single Nucleotide Variants
Discussion
Prenatal Expression of ASD-Associated Genes
Prenatal Expression of Schizophrenia-Associated Genes
Future Transcriptome Investigations
Footnote
Supplementary Material
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