Table 2.
Top-ranked schizophrenia-associated differentially methylated positions (DMPs). Shown are DMPs associated with schizophrenia 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 schizophrenia-associated DMPs for each of the four brain regions profiled are presented in Supplementary Materials, Tables S2–S5. 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. Note hippocampus tissue was not available from the DBCBB.
| Probe ID | Genomic position (hg19) | Illumina gene annotation | Genic region | GREAT annotation (38) | Brain region | DNA methylation difference (%) | P | DNA methylation difference (%) LNDBB | P-value LNDBB | DNA methylation difference (%) DBCBB | P-value DBCBB |
|---|---|---|---|---|---|---|---|---|---|---|---|
| cg08743050 | chr11:113113936 | NCAM1 | Body | TTC12; NCAM1 | Prefrontal cortex | −3.80 | 1.84E-08 | −1.80 | 0.15 | −4.63 | 8.39E-09 |
| cg14609448 | chr21:34896882 | GART | Body; 3'UTR | DNAJC28; GART | Cerebellum | 2.29 | 2.48E-08 | 1.37 | 0.02 | 3.11 | 3.60E-08 |
| cg08103144 | chr5:150028986 | SYNPO | Body | MYOZ3; SYNPO | Striatum | −3.17 | 3.64E-08 | 0.08 | 0.94 | −4.43 | 6.61E-11 |
| cg03847432 | chr7:43391524 | HECW1 | Body | STK17A; HECW1 | Striatum | 2.71 | 5.23E-08 | 1.55 | 0.04 | 3.69 | 4.76E-08 |
| cg22182016 | chr15:57998894 | GRINL1A; GCOM1 | TSS200; Body | POLR2M | Striatum | −0.51 | 5.67E-08 | −0.27 | 0.14 | −0.59 | 5.41E-08 |
| cg01757160 | chr12:96588951 | ELK3 | 5'UTR | ELK3 | Cerebellum | 0.57 | 5.74E-08 | 0.58 | 5.13E-04 | 0.56 | 3.04e-05 |
| cg25361651 | chr20:29847402 | DEFB115 | Body | DEFB115; DEFB116 | Striatum | 4.43 | 6.52E-08 | 2.27 | 0.10 | 5.63 | 3.67E-08 |
| cg22221320 | chr1:89664340 | GBP4 | Body | GBP4 | Striatum | 6.93 | 7.88E-08 | 2.39 | 0.23 | 10.24 | 1.58E-09 |
| cg07751266 | chr16:67515323 | ATP6V0D1 | TSS1500 | ATP6V0D1 | Hippocampus | −1.35 | 1.27E-07 | −1.35 | 1.27E-07 | – | – |
| cg09757430 | chr13:28397122 | - | – | PDX1; GSX1 | Cerebellum | −3.13 | 1.37E-07 | −2.38 | 0.02 | −3.54 | 1.65E-06 |
| cg05686445 | chr7:127636396 | C7orf54; SND1 | TSS1500; Body | LRRC4; SND1 | Prefrontal cortex | −3.65 | 1.63E-07 | −2.04 | 0.07 | −4.67 | 1.57E-07 |
| cg20751795 | chr19:58281019 | ZNF586 | TSS200 | ZNF586 | Cerebellum | 0.57 | 1.64E-07 | 0. 42 | 1.17E-06 | 0.13 | 0.03 |