Table 4.
Top-ranked differentially methylated positions (DMPs) associated with schizophrenia polygenic score (PRS). Shown are DMPs associated with the schizophrenia PRS at a highly stringent significance threshold (P < 1.66E-07) derived using permutations to estimate the nominal P-value for 5% family-wise error. Top-ranked PRS-associated DMPs for each of the four brain regions profiled are presented in Supplementary Materials, Tables S12–S15. The methylation difference is measured per PRS unit. Illumina and Genomic Regions Enrichment of Annotation Tool (GREAT) (38) annotation is listed for each DMP. LNDBB = London Neurodegenerative Disorders Brain Bank; DBCBB = Douglas-Bell Canada Brain Bank.
| Probe ID | Genomic position (hg19) | Illumina gene annotation | Gene region | GREAT annotation (38) | Brain region | DNA methylation change (%) | P | DNA methylation change (%) LNDBB | P-value LNDBB | DNA methylation change (%) DBCBB | P-value DBCBB |
|---|---|---|---|---|---|---|---|---|---|---|---|
| cg18847009 | chr2:70175826 | – | – | ASPRV1; MXD1 | Prefrontal cortex | −0.51 | 8.98E-08 | −0.50 | 7.14E-07 | −0.66 | 0.03 |
| cg26893445 | chr15:85924187 | AKAP13 | 5'UTR | AKAP13 | Striatum | 0.15 | 6.73E-08 | 0.16 | 6.80E-08 | 0.03 | 0.21 |
| cg12595281 | chr15:93633172 | RGMA | TSS1500 | RGMA | Striatum | 0.68 | 6.85E-08 | 0.82 | 5.36E-10 | 0.13 | 0.07 |
| cg20640266 | chr9:116811789 | ZNF618 | Body | AMBP; ZNF618 | Cerebellum | 0.60 | 1.62E-09 | 0.74 | 2.06E-06 | 0.32 | 0.02 |
| cg27150552 | chr7:48026856 | SUNC1 | 3'UTR | HUS1; SUN3 | Cerebellum | 0.34 | 1.30E-08 | 0.36 | 6.44E-09 | 0.09 | 0.68 |
| cg05209768 | chr2:164573665 | FIGN | Body | KCNH7; FIGN | Cerebellum | 0.70 | 1.55E-08 | 0.70 | 1.31E-07 | 0.70 | 0.04 |
| cg07793808 | chr12:122019006 | KDM2B | TSS200; TSS1500 | KDM2B | Cerebellum | −0.19 | 1.66E-08 | −0.21 | 2.94E-04 | −0.17 | 1.28E-05 |
| cg10218777 | chr3:133180261 | BFSP2 | Body | CDV3; BFSP2 | Cerebellum | 0.67 | 3.86E-08 | 0.65 | 4.24E-07 | 0.86 | 0.03 |
| cg01682070 | chr16:29996774 | TAOK2 | Body | HIRIP3; TAOK2 | Cerebellum | 0.32 | 4.20E-08 | 0.37 | 1.21E-08 | 0.11 | 0.38 |
| cg11786558 | chr17:2266589 | SGSM2 | Body | SGSM2; MNT | Cerebellum | 0.69 | 4.35E-08 | 0.84 | 1.23E-06 | 0.52 | 4.73E-03 |
| cg26053083 | chr11:14995770 | – | – | CALCA | Cerebellum | −0.15 | 4.41E-08 | −0.15 | 2.53E-06 | −0.14 | 4.95E-03 |
| cg01022840 | chr14:71250264 | MAP3K9 | Body | MAP3K9; TTC9 | Cerebellum | 0.63 | 7.86E-08 | 0.66 | 7.10E-07 | 0.53 | 0.04 |
| cg08478539 | chr15:68640339 | ITGA11 | Body | FEM1B; ITGA11 | Cerebellum | 0.69 | 1.06E-07 | 0.80 | 3.06E-07 | 0.45 | 0.06 |
| cg23788334 | chr2:137181176 | – | – | THSD7B; CXCR4 | Cerebellum | −0.13 | 1.15E-07 | −0.15 | 1.45E-05 | −0.11 | 1.56E-03 |
| cg16904520 | chr2:230590962 | – | – | DNER; TRIP12 | Cerebellum | 0.26 | 1.25E-07 | 0.27 | 2.06E-06 | 0.22 | 0.02 |