Table 1.
Associations between common PTP4A1-PHF3-EYS variants and different neuropsychiatric disorders
| Human Diseases | Ethnicity | Design | Dataset name | SNP # (total) |
SNP
# (p<0.05) |
SNP
# (p<α) |
Minimal p value |
Most sig. SNP | Gene | Affected |
Unaffected |
||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| N | MAF | N | MAF | ||||||||||
| Alcoholism | AA | CC | SAGE+COGA | 1095 | 289 | 56 | 1.9×10-6 | rs7742595 | 5’ to PTP4A1 | 681 | 0.249 | 508 | 0.167 |
| Alcoholism | EA | CC | SAGE+COGA | 762 | 272 | 0 | 3.9×10-4 | rs10755416 | 5’ to PTP4A1 | 1409 | 0.456 | 1518 | 0.408 |
| Alcoholism | EAu | Fam | OZ-ALC | 734 | 42 | 0 | 4.5×10-3 | rs2347978 | 5’ to PTP4A1 | 1645 | 0.074 | 1645 | 0.135 |
| Bipolar Disorder | EA | CC | BDO+GRU | 719 | 248 | 0 | 2.4×10-5 | rs504776 | EYS | 368 | 0.316 | 1034 | 0.417 |
| Bipolar Disorder | EA | CC | BARD+GRU | 718 | 183 | 0 | 3.5×10-4 | rs1057530 | PHF3-EYS | 653 | 0.419 | 1034 | 0.491 |
| Bipolar Disorder | AA | CC | BARD+GRU | 825 | 4 | 0 | 0.026 | rs1482444 | EYS | 141 | 0.177 | 671 | 0.391 |
| ADHD | CA | Fam | IMAGE | 768 | 63 | 0 | 9.2×10-5 | rs10943832 | 5’ to PTP4A1 | 924 | 0.137 | 924 | 0.421 |
| Schizophrenia | EA | CC | MGS_nonGAIN | 702 | 6 | 0 | 0.022 | rs114419825 | EYS | 1437 | 0.092 | 1347 | 0.056 |
| Schizophrenia | EA | CC | GAIN | 717 | 56 | 0 | 5.4×10-4 | rs1723533 | 5’ to PTP4A1 | 1351 | 0.064 | 1378 | 0.101 |
| Schizophrenia | AA | CC | GAIN | 805 | 58 | 0 | 3.4×10-4 | rs76384923 | EYS | 1195 | 0.476 | 954 | 0.330 |
| Autism | EA | Fam | AGP | 720 | 22 | 0 | 1.7×10-4 | rs9351126 | EYS | 1330 | 0.169 | 1330 | 0.252 |
| Major Depression | CA | CC | PRSC | 730 | 57 | 0 | 2.5×10-4 | rs7753631 | EYS | 1805 | 0.282 | 1820 | 0.324 |
| Alzheimer’s Disease | CA | Fam | LOAD × 4 | 802 | 6 | 0 | 0.015 | rs2624662 | EYS | 2298 | 0.288 | 2298 | 0.313 |
| Alzheimer’s disease | EA | CC | GenADA | 477 | 1 | 0 | 0.045 | rs1779776 | 5’ to PTP4A1 | 806 | 0.057 | 782 | 0.075 |
| ALS | CA | CC | GRU | 540 | 79 | 0 | 0.008 | rs1711920 | 5’ to PTP4A1 | 261 | 0.250 | 246 | 0.330 |
| Early Onset Stroke | EA | CC | GEOS × 3 | 749 | 29 | 0 | 0.007 | rs6915363 | EYS | 372 | 0.114 | 430 | 0.064 |
| Early Onset Stroke | AA | CC | GEOS × 3 | 1042 | 10 | 0 | 0.014 | rs9362331 | EYS | 309 | 0.353 | 290 | 0.435 |
| Ischemic Stroke | CA | CC | ISGS | 722 | 3 | 0 | 0.020 | rs3003669 | EYS | 219 | 0.370 | 266 | 0.298 |
| Parkinson’s Disease | CA | CC | NGRC | 753 | 4 | 0 | 0.004 | rs6900114 | EYS | 2000 | 0.099 | 1986 | 0.125 |
| Parkinson’s Disease | CA | CC | PDRD+GRU | 711 | 1 | 0 | 0.046 | rs1681939 | 5’ to PHF3 | 900 | 0.093 | 867 | 0.114 |
| Parkinson’s Disease | CA | CC | lng_coriell_pd | 765 | 254 | 0 | 0.004 | rs13213141 | 3’ to PTP4A1 | 940 | 0.200 | 801 | 0.249 |
Only the most significant risk markers are listed. The significance level (α) is set at 1.6×10-5 based on correction for the numbers of effective genetic markers (calculated by SNPSpD) and the number of cohorts (i.e., 21). N, sample size; MAF, minor allele frequency; AA, African-American; EA, European-American; EAu, European-Australian; CA, Caucasian; CC, case-control design; Fam, family-based design. ADHD, Attention deficit hyperactivity disorder; ALS, Amyotrophic Lateral Sclerosis. Dataset names correspond to dbGaP. In family-based cohorts, N= sample size of affected offspring; “affected MAF”=“transmitted MAF”, “unaffected MAF”=“untransmitted MAF” in offspring.