Table 2.
Targeted Genetic Variants
| Gene | refSNP | Method | Total Calls, No. (%) | Target Versus Nontarget Genotype | Wild Type |
Heterozygous |
Homozygous |
|||
|---|---|---|---|---|---|---|---|---|---|---|
| No. (%) | No. (%) | No. (%) | ||||||||
| Genes Related to Folate Metabolism | ||||||||||
| MTHFR | 1801131 | iPLEX | 295 (84%) | AC/CC v AA | AA | 152 (51%) | AC | 117 (40%) | CC | 26 (9%) |
| MTHFR | 1801133 | TaqMan | 274 (78%) | TT v CC/CT | CC | 100 (36%) | CT | 142 (52%) | TT | 32 (12%) |
| SLC19A1 | 1051266 | iPLEX | 283 (81%) | AA v AG/GG | GG | 81 (29%) | AG | 131 (46%) | AA | 71 (25%) |
| TCN2 | 1801198 | iPLEX | 307 (88%) | GG v CC/CG | CC | 113 (37%) | CG | 136 (44%) | GG | 58 (19%) |
| TS | 28bp repeat | PCR | 207 (69%)* | 3R/3R v 2R/2R or 2R/3R | 2R/2R | 36 (17%) | 2R/3R | 133 (64%) | 3R/3R | 38 (18%) |
| Genes Related to Glucocorticoids | ||||||||||
| ABCB1 | 1045642 | iPLEX | 301 (86%) | TT v CC/CT | CC | 91 (30%) | CT | 140 (47%) | TT | 70 (23%) |
| NR3C1 | 41423247 | iPLEX | 296 (85%) | CG/GG v CC | CC | 123 (42%) | CG | 140 (47%) | GG | 33 (11%) |
| Genes Related to Neurotransmission | ||||||||||
| COMT | 4680 | TaqMan | 280 (80%) | AA v AG/GG | GG | 76 (27%) | AG | 161 (58%) | AA | 43 (15%) |
| GRIN2B | 10193895 | iPLEX | 302 (86%) | AG/GG v AA | AA | 279 (92%) | AG | 22 (7%) | GG | 1 (1%) |
| MAOA | 1137070 | TaqMan | 267 (76%) | CT/TT v CC | CC | 159 (60%) | CT | 55 (21%) | TT | 53 (20%) |
| SLC6A4 | 1042173 | TaqMan | 243 (69%) | AA v CA/CC | CC | 43 (18%) | CA | 135 (56%) | AA | 65 (27%) |
| Genes Related to Inflammation or Oxidative Damage | ||||||||||
| APOE | 7412 | TaqMan | 281 (80%) | CT/TT v CC | CC | 242 (86%) | CT | 39 (14%) | TT | 0 (0%) |
| APOE | 429358 | TaqMan | 325 (93%) | CC/CT v TT | TT | 249 (77%) | TC | 73 (22%) | CC | 3 (1%) |
| GSTP1 | 1138272 | TaqMan | 280 (80%) | CT/TT v CC | CC | 220 (79%) | CT | 48 (17%) | TT | 12 (4%) |
| GSTP1 | 1695 | TaqMan | 251 (72%) | AG/GG v AA | AA | 121 (48%) | AG | 111 (44%) | GG | 19 (8%) |
| HFE | 1799945 | iPLEX | 304 (87%) | CG/GG v CC | CC | 235 (77%) | CG | 63 (21%) | GG | 6 (2%) |
| HFE | 1800562 | iPLEX | 302 (86%) | AA/AG v GG | GG | 269 (89%) | AG | 33 (11%) | AA | 0 (0%) |
| IL1B | 1143627 | TaqMan | 269 (77%) | GG v AA/AG | AA | 104 (39%) | AG | 73 (27%) | GG | 92 (34%) |
| IL1B | 1143634 | TaqMan | 327 (93%) | AA v AG/GG | GG | 175 (54%) | AG | 100 (31%) | AA | 52 (16%) |
| IL1RN | 380092 | TaqMan | 291 (83%) | TT v AA/AT | AA | 131 (45%) | AT | 123 (42%) | TT | 37 (13%) |
| NOS3 | 1799983 | iPLEX | 300 (86%) | TT v GG/GT | GG | 137 (46%) | GT | 133 (44%) | TT | 30 (10%) |
| NQO1 | 1800566 | TaqMan | 312 (89%) | CT/TT v CC | CC | 189 (61%) | CT | 115 (37%) | TT | 8 (3%) |
| SLCO2A1 | 7625035 | iPLEX | 300 (86%) | AG/GG v AA | AA | 182 (61%) | AG | 93 (31%) | GG | 25 (8%) |
NOTE. Targeted genetic variants studied in 350 patients with neurocognitive data. Twenty-three genetic polymorphisms were included in these analyses. The number of patients in whom a genotype could be called is indicated, along with the observed distribution of genotypes. The target genotypes, hypothesized to be associated with increased risk of inferior neurocognitive outcomes, are indicated.
Abbreviations: PCR, polymerase chain reaction; SNP, single nucleotide polymorphism.
*
For analysis of TS, sufficient DNA remained for testing in 301 cases.