Table 5.
TDT analysis for SNPs and haplotypes in candidate genes previously reported in the literature as being associated with PCOS
| Gene tested (Ref.) | SNP tested | Major/ minor alleles (+ strand) | Literature studies
|
TDT results
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of cases: controls | Population | Reported association: P value | Allele | T | Not T | Total | Transmission frequency | TDT χ2 | P value | |||
| ADIPOQ (25) | rs2241766 | T/G | 143:245 | Finland | ns | T | 46 | 44 | 90 | 0.511 | 0.04 | 0.841 |
| rs1501299 | G/T | T reduced frequency: 0.047 | T | 193 | 160 | 353 | 0.547 | 3.09 | 0.079 | |||
| Haplotype | ns | TT | 114.8 | 95.9 | 210.7 | 0.545 | 1.70 | 0.192 | ||||
| CAPN5 (21) | rs948976 | A/G | 148:606 | Spain | ns | G | 184 | 169 | 353 | 0.521 | 0.64 | 0.425 |
| rs4945140 | G/A | ns | G | 219 | 212 | 431 | 0.508 | 0.11 | 0.736 | |||
| rs2233546 | C/T | ns | T | 44 | 39 | 83 | 0.530 | 0.30 | 0.583 | |||
| rs2233549 | G/A | ns | A | 159 | 152 | 311 | 0.511 | 0.16 | 0.691 | |||
| Haplotype | GGCA: 0.009 | GGCA | 49.3 | 44.5 | 93.8 | 0.526 | 0.24 | 0.623 | ||||
| Haplotype | GGTG: 0.001 | GGTG | 25.3 | 20.5 | 45.8 | 0.552 | 0.50 | 0.478 | ||||
| ENPP1/ PC1 (26) | rs1044498 | A/C | 143:115 | Finland | AC or CC: <0.01 | A | 131 | 104 | 235 | 0.557 | 3.10 | 0.078 |
| EPHX1 (29) | rs1051740 | T/C | 112:115 | Finland | ns | C | 196 | 179 | 375 | 0.523 | 0.77 | 0.380 |
| rs2234922 | A/G | ns | G | 86 | 72 | 158 | 0.544 | 1.24 | 0.265 | |||
| Haplotype | CG: 0.026 | CG | 35.2 | 48.3 | 83.5 | 0.422 | 0.92 | 0.338 | ||||
| FEM1A (22) | rs1044386 | G/A | 287:187 | United States (Alabama) | 0.013 | A | 158 | 146 | 304 | 0.520 | 0.474 | 0.491 |
| rs8111933 | C/G | 0.001 | G | 217 | 215 | 432 | 0.502 | 0.01 | 0.924 | |||
| Haplotype | AC: 0.013 | AC | 162.8 | 154.7 | 317.5 | 0.513 | 0.21 | 0.651 | ||||
| Haplotype | GG: 0.001 | GG | 226.3 | 229.1 | 455.4 | 0.497 | 0.02 | 0.897 | ||||
| FEM1B (22) | rs10152450 | T/G | 287:187 | United States (Alabama) | G reduced frequency: 0.005 | T | 239 | 191 | 430 | 0.556 | 5.36 | 0.021 |
| rs6494730 | G/T | ns | G | 215 | 175 | 390 | 0.551 | 4.10 | 0.043 | |||
| Haplotype | G(GAA)T: 0.004 | GT | 197 | 238 | 435 | 0.453 | 3.86 | 0.049 | ||||
| H6PD (30) | rs6688832 | G/A | 116:76 | Spain | Genotype frequency: 0.011 | G | 178 | 166 | 344 | 0.517 | 0.42 | 0.517 |
| HSD17B6 (27) | rs898611 | T/C | 173:107 | Australia | T reduced frequency: 0.03 | T | 218 | 208 | 426 | 0.512 | 0.24 | 0.628 |
| IL1A (28) | rs1800587 | G/A | 105:102 | Austria | Genotype frequency: 0.04 | A | 190 | 189 | 379 | 0.501 | 0.00 | 0.956 |
| SGTA (24) | rs2238614 | G/A | 287:187 | United States (Alabama) | ns | G | 175 | 134 | 309 | 0.566 | 5.44 | 0.020 |
| rs741103 | T/C | ns | T | 140 | 118 | 258 | 0.543 | 1.88 | 0.171 | |||
| rs1640262 | T/C | CC protective: 0.009 | Did not genotype | |||||||||
| rs1005556a | G/T | G | 181 | 144 | 325 | 0.557 | 4.21 | 0.040 | ||||
| Haplotype | GAT: 0.015 | GTG | 216.4 | 164.5 | 380.9 | 0.568 | 7.08 | 0.008 | ||||
| SRD5A1 (23) | rs3797179 | G/A | 287:187 | United States (Alabama) | ns | Did not genotype | ||||||
| rs6872996b | C/T | C | 193 | 172 | 365 | 0.529 | 1.21 | 0.272 | ||||
| rs39848 | T/C | ns | T | 231 | 205 | 436 | 0.530 | 1.55 | 0.213 | |||
| Haplotype | TA: 0.03 | TC | 182.6 | 200.1 | 382.7 | 0.477 | 0.80 | 0.371 | ||||
| (Continued) | ||||||||||||