Table 2. Twenty-five schizophrenia candidate genes were checked for association with schizophrenia in a cohort of 879 cases and 864 controls.
| Gene | Previously associated SNPs present on Illumina chip | Previously associated SNP represented by an LD proxy on Illumina chip | Closest proxy (r2 in CEU) | SNP replication p | OR excluded | Lowest p | #SNPs tested in gene | Gene-wide correction | Set-wide correction | Genome-wide correction |
| AKT1 | NA | NA | 0.416 | 4 | 1 | 1 | 1 | |||
| CAPON/NOS1AP | NA | NA | 0.033 | 45 | 1 | 1 | 1 | |||
| CHRNA7 | NA | NA | 0.067 | 14 | 0.94 | 1 | 1 | |||
| COMT | rs4680 | 0.94 | 1.05 | 0.090 | 12 | 1 | 1 | 1 | ||
| DAO | NA | NA | 0.288 | 9 | 1 | 1 | 1 | |||
| DAOA(G72) | rs3916971 rs778293 | 0.09 | 1.23 | 0.085 | 10 | 0.85 | 1 | 1 | ||
| DISC1 | rs2295959 rs3738401 | 0.621 | 1.14 | 0.082 | 64 | 1 | 1 | 1 | ||
| DRD2 | rs6277 rs6275 | rs754672 (0.81) rs2242592(1) | 0.753 | 1.12 | 0.033 | 14 | 0.46 | 1 | 1 | |
| DRD3 | rs6280 | 0.491 | 1.15 | 0.168 | 13 | 1 | 1 | 1 | ||
| DTNBP1 | rs760761 | rs1474605 (1) | 0.948 | 1.05 | 0.107 | 18 | 1 | 1 | 1 | |
| ERBB4 | rs7598440 rs707284 | rs839523 rs4673628 | rs839517 (0.86) rs1851169(1) | 0.313 | 1.18 | 0.012 | 181 | 1 | 1 | 1 |
| FEZ1 | NA | NA | 0.002 | 13 | 0.026 | 1 | 1 | |||
| GAD1 | NA | NA | 0.289 | 9 | 1 | 1 | 1 | |||
| GRIK4 | NA | NA | 0.028 | 54 | 1 | 1 | 1 | |||
| GRM3 | rs1468412 | rs2237562 (1) | 0.495 | 1.15 | 0.075 | 27 | 1 | 1 | 1 | |
| HTR2A | rs6313 | rs4941573 (1) | 0.498 | 1.15 | 0.042 | 21 | 0.88 | 1 | 1 | |
| MRDS1(OFCC1) | NA | NA | 0.017 | 36 | 0.61 | 1 | 1 | |||
| MUTED | NA | NA | 0.035 | 31 | 1 | 1 | 1 | |||
| NOTCH4 | rs175174 | rs11089328(0.93) | 0.872 | 1.09 | 0.0017 | 28 | 0.048 | 1 | 1 | |
| NRG1 | NA | NA | 0.012 | 157 | 1 | 1 | 1 | |||
| PPP3CC | NA | NA | 0.228 | 6 | 1 | 1 | 1 | |||
| PRODH2 | NA | NA | 0.163 | 7 | 1 | 1 | 1 | |||
| RGS4 | rs951439 | rs6678136 (1) | 0.186 | 1.20 | 0.186 | 2 | 0.372 | 1 | 1 | |
| TNF | NA | NA | 0.248 | 5 | 1 | 1 | 1 | |||
| ZDHHC8 | rs175174 | rs11089328 (0.93) | 0.872 | 1.09 | 0.794 | 2 | 1 | 1 | 1 |
Displayed are (1) gene symbol; (2) previously associated candidate SNPs in that gene, included in the Illumina 300K chip; (3) previously associated candidate SNPs in that gene, not included in the Illumina 300K chip but can be represented by a LD proxy in the chip; (4) the closest proxy SNP present on the Illumina 300K chip for column 3; (5) the lowest p value for SNP-specific (column 2 and 4) replication; (6) Maximum odds ratio (allelic OR under multiplicative genetic model) at the previously-implicated locus, based on observed p value at this SNP or a proxy. A real odds ratio of this size is expected to produce a p value as high as the one observed only 5% of the time, based on the power formulae of Chapman et al [59]; For detailed review on the previous reports of these candidate genes and SNPs see reference [30]; (7) lowest p value of all the HumanHap300 SNPs located in that gene (lowest p); (8) number of SNPs tested in each gene; (9) the lowest p value corrected for all the SNPs tested in that gene (gene-wide correction); (10) the lowest p value corrected for all the SNPs in the 25 candidate genes (set-wide correction); (11) the lowest p value after correction for all HumanHap300 SNPs tested (genome-wide correction).