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Reference | Saito T., 2014 PMID: 24888570 |
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Citation | Saito, T., et al. (2014). "Replication and cross-phenotype study based upon schizophrenia GWASs data in the Japanese population: Support for association of MHC region with psychosis." Am J Med Genet B Neuropsychiatr Genet. |
Disease Type | Bipolar Disorder & Schizophrenia |
Study Design | case-control |
Study Type | Genome-wide association study |
Sample Size | 1032 SCZ, 1012 BD(BD typeI=621, BD typeII=380, schizoaffective disorder [SA]=7, BD type information not available=4) and 993 controls. |
SNP/Region/Marker Size | 51 SNPs |
Predominant Ethnicity | Mongloid |
Population | Japanese |
Gender | The first-set: BD: 51.8% female subjects of 1,012 patients; SZ: 48.3% female subjects of 1,032 patients; Controls: 51.1% female subjects of 993 healthy controls. The replication set: BD: 54.6% female subjects of 821 patients, SD=14.4; SZ: 45.1% female subjects of 1,808 patients; Controls: 57.2% female subjects of 2,321 healthy controls. |
Age Group | adults : The first-set: BD: mean age=50.7, SD=14.3; SZ: mean age=46.8, SD=14.8; Controls: mean age=49.7, SD=14.0. The replication set: BD: mean age=48.2, SD=14.4; SZ: mean age=49.8, SD=14.8; Controls: mean age=42.3, SD=14.2. |
Sample Diagnosis | DSM-IV |
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Sample Status | All subjects were unrelated to each other and ethnically Japanese. Patients with bipolar disorder (BD) were collected at each university participating in the Collaborative Study of Mood Disorder (COSMO). The patients with schizophrenia (SCZ) were collected at Fujita Health University and Okayama University. The patients were diagnosed according to DSM-IV criteria with the consensus of at least two experienced psychiatrists based on unstructured interviews and a review of medical records. |
Replication Size | 1808 SCZ, 821 BD(BD type I =387, BD type II = 344, SA=89, unknown type of diagnosis=1) and 2321 controls |
Technique | All SNPs were genotyped using the Sequenom iPLEX Gold system (Sequenom, San Diego, CA). |
Statistical Method | All statistical procedures were performed using PLINK version 1.07.We assessed the allelic association(two-tailed) of the selected SNPs and the three phenotypes. To account for linkage disequilibrium (LD) between SNPs selected for the analysis, we used the Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) interface to identify a sufficient number of independent variables for the first-set screening analysis (N=42). Ameta-analysis of the SNPs was conducted by combining the screening and replication datasets. A binary effects model, one of the novel random effects approaches, which is providing more statistical power under the existence of heterogeneity, was applied in each analysis using METASOFT program. |
Result Summary | Nine SNPs revealed nominal association signals for all comparisons (Puncorrected<0.05), of which two SNPs located in the major histocompatibility complex region(rs7759855in zinc finger and SCAN domain containing 31 [ZSCAN31] and rs1736913 in HLA-F antisense RNA1 [HLA-F-AS1]) were further assessed in the second-set replication samples. The associations were confirmed for rs7759855 (Pcorrected=0.026 for psychosis; Pcorrected=0.032 for SCZ), although the direction of effect was opposite to that in the original GWAS of the Chinese population. Finally, a meta-analysis was conducted using our two samples and using our data and data from PsychiatricGWASConsortium (PGC), which have shown the same direction of effect. SNP in ZSCAN31(rs7759855) had the strongest association with the phenotypes(best P=6.8*10-5 for psychosis: present plus PGC results). |
SNP | Related Gene(s) | Allele Change | Risk Allele | Statistical Values | Author Comments | Result Category |
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rs4775413 | CYCSP38 | T/C | First-set screening: P-valuecorrected=1, P-value=0.0731, OR=1.13, 95%CI=0.99-1.29 | No significant association was observed. No significant association was observed. | Negative | |
rs1060041 | DCAF6 | T/C | First-set screening: P-valuecorrected=1, P-value=0.749, OR=1.03, 95%CI=0.85-1.25 | No significant association was observed. No significant association was observed. | Negative | |
rs10489202 | MPC2 DCAF6 | T/G | First-set screening: P-valuecorrected=1, P-value=0.901, OR=1.01, 95%CI=0.83-1.23 | No significant association was observed. No significant association was observed. | Negative | |
rs1233710 | ZKSCAN4 | T/C | First-set screening: P-valuecorrected=1, P-value=0.0459, OR=1.15, 95%CI=1.00-1.31 | Significant association was observed. Significant association was observed. | Positive | |
rs7759855 | ZSCAN31 | G/A | First-set screening: P-valuecorrected=0.012, P-value=2.82*10-4, OR=1.6, 95%CI=1.24-2.07; Second-set replication: P-valuecorrected=0.249, P-value=0.125, OR=1.19, 95%CI=0.95-1.8. Current study (first-set screening_second-set replication): P-value=2.70*10-4, I2=67.7 | Significant association was observed. Significant association was observed. | Positive | |
rs1736913 | HLA-F-AS1 HLA-F | A/G | First-set screening: P-valuecorrected=0.019, P-value=4.63*10-4, OR=1.31, 95%CI=1.13-1.52; Second-set replication: P-valuecorrected=0.214, P-value=0.107, OR=1.12, 95%CI=0.98-1.27. Current study (first-set screening_second-set replication): P-value=4.29*10-4, I2=59.0 | Significant association was observed. Significant association was observed. | Positive | |
rs6927023 | GPX6 | A/G | First-set screening: P-valuecorrected=0.056, P-value=0.00132, OR=1.52, 95%CI=1.18-1.96 | Significant association was observed. Significant association was observed. | Positive | |
rs7004633 | MMP16 | G/A | First-set screening: P-valuecorrected=1, P-value=0.384, OR=0.93, 95%CI=0.80-1.09 | No significant association was observed. No significant association was observed. | Negative | |
rs2021722 | TRIM26 | A/G | First-set screening: P-valuecorrected=0.28, P-value=0.00678, OR=0.76, 95%CI=0.62-0.93 | Significant association was observed. Significant association was observed. | Positive |
Gene | Statistical Values/Author Comments | Result Category |
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TRIM26 | The associated SNP in this gene showed significant association with BD. The associated SNP in this gene showed significant association with BD. | Positive |
HLA-F-AS1 | The associated SNP in this gene showed significant association with BD. The associated SNP in this gene showed significant association with BD. | Positive |
GPX6 | The associated SNP in this gene showed significant association with BD. The associated SNP in this gene showed significant association with BD. | Positive |
ZKSCAN4 | The associated SNP in this gene showed significant association with BD. The associated SNP in this gene showed significant association with BD. | Positive |
CYCSP38 | The associated SNP in this gene showed no significant association with BD. The associated SNP in this gene showed no significant association with BD. | Negative |
MMP16 | The associated SNP in this gene showed no significant association with BD. The associated SNP in this gene showed no significant association with BD. | Negative |
ZSCAN31 | The associated SNP in this gene showed significant association with BD. The associated SNP in this gene showed significant association with BD. | Positive |
DCAF6 | The associated SNP in this gene showed no significant association with BD. The associated SNP in this gene showed no significant association with BD. | Negative |
MPC2 | The associated SNP in this gene showed no significant association with BD. The associated SNP in this gene showed no significant association with BD. | Negative |
Disease | SNP | Related Gene(s) | Statistical Values | Description | Result Category |
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SZ | rs7759855 | ZSCAN31 | First-set screening: P-valuecorrected=0.12, P-value=0.00292, OR=1.48, 95%CI=1.14-1.91; Second-set replication: P-valuecorrected=0.0322, P-value=0.0161, OR=1.23, 95%CI=1.04-1.46. Current study (first-set screening_second-set replication): P-value=6.65*10-4, I2=25.4; PGC+current study: P-value=5.02*10-4, I2=0.0. | Significant association was observed. | Positive |
SZ | rs1233710 | ZKSCAN4 | First-set screening: P-valuecorrected=1, P-value=0.534, OR=1.04, 95%CI=0.91-1.19 | No significant association was observed. | Negative |
SZ | rs10489202 | MPC2 DCAF6 | First-set screening: P-valuecorrected=1, P-value=0.0267, OR=1.24, 95%CI=1.02-1.49 | Significant association was observed. | Positive |
SZ | rs1060041 | DCAF6 | First-set screening: P-valuecorrected=1, P-value=0.0481, OR=1.21, 95%CI=1.00-1.46 | Significant association was observed. | Positive |
SZ | rs4775413 | CYCSP38 | First-set screening: P-valuecorrected=0.65, P-value=0.0156, OR=1.18, 95%CI=1.03-1.34 | Significant association was observed. | Positive |
SZ | rs7004633 | MMP16 | First-set screening: P-valuecorrected=0.65, P-value=0.0155, OR=0.83, 95%CI=0.71-0.96 | Significant association was observed. | Positive |
SZ | rs2021722 | TRIM26 | First-set screening: P-valuecorrected=0.32, P-value=0.00759, OR=0.76, 95%CI=0.62-0.93 | Significant association was observed. | Positive |
SZ | rs1736913 | HLA-F-AS1 HLA-F | First-set screening: P-valuecorrected=0.89, P-value=0.0212, OR=1.19, 95%CI=1.03-1.39; Second-set replication: P-valuecorrected=0.0866, P-value=0.0433, OR=1.11, 95%CI=1.00-1.23. Current study (first-set screening_second-set replication): P-value=0.00800, I2=0.0; PGC+current study: P-value=0.00445, I2=59.7 | Significant association was observed. | Positive |
SZ | rs6927023 | GPX6 | First-set screening: P-valuecorrected=0.16, P-value=0.00384, OR=1.46, 95%CI=1.13-1.88 | Significant association was observed. | Positive |
Disease | Gene | Description | Result Category |
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SZ | HLA-F-AS1 | The associated SNP in this gene showed significant association with SZ. | Positive |
SZ | CYCSP38 | The associated SNP in this gene showed significant association with SZ. | Positive |
SZ | TRIM26 | The associated SNP in this gene showed significant association with SZ. | Positive |
SZ | DCAF6 | The associated SNP in this gene showed significant association with SZ. | Positive |
SZ | ZKSCAN4 | The associated SNP in this gene showed no significant association with SZ. | Negative |
SZ | MMP16 | The associated SNP in this gene showed significant association with SZ. | Positive |
SZ | MPC2 | The associated SNP in this gene showed significant association with SZ. | Positive |
SZ | GPX6 | The associated SNP in this gene showed no association with SZ. | Positive |
SZ | ZSCAN31 | The associated SNP in this gene showed significant association with SZ. | Positive |
Copyright: Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences Feedback
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Last update: March 31, 2016