Table 2.
Genotype and Allele Frequencies of 10 Assessed Single-Nucleotide Polymorphisms in a Cohort of 407 Saudi Individuals (156 With Head and Neck Cancer and 251 Controls Without Cancer)
| |
Total samples: 407 |
|
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|---|---|---|---|---|---|---|
| Gene, genotype, and allele | Cancer(n=156) (%) | Control(n=251) (%) | Odds ratio (95% confidence interval) | Significance level p | Overall frequencies (%) | NCBI frequencies (%)a |
| p21 (CDKN1A) codon 31 C>A Ser/Arg | ||||||
| C/C | 87 (56) | 166 (66) | 62 | 55 | ||
| C/A | 61 (39) | 77 (31) | 1.51 (0.99–2.31) | 0.06 | 33 | 32 |
| A/A | 8 (5) | 8 (3) | 1.91 (0.69–5.25) | 0.28 | 5 | 13 |
| C | 235 (75) | 409 (81) | 79 | 71 | ||
| A | 77 (25) | 93 (19) | 1.44 (1.02–2.03) | 0.041 | 21 | 29 |
| p53 (TP53) codon 72 G>C Arg/Pro | ||||||
| G/G | 48 (31) | 71 (28) | 29 | 36 | ||
| G/C | 70 (45) | 110 (44) | 0.94 (0.59–1.51) | 0.81 | 44 | 41 |
| C/C | 38 (24) | 70 (28) | 0.80 (0.47–1.38) | 0.49 | 27 | 23 |
| G | 166 (53) | 252 (50) | 51 | 56 | ||
| C | 146 (47) | 250 (50) | 0.89 (0.67–1.18) | 0.43 | 49 | 44 |
| ATM codon 1853 G>A Asp/Asn | ||||||
| G/G | 131 (84) | 218 (87) | 85.5 | 88.7 | ||
| G/A | 23 (15) | 33 (13) | 1.15 (0.65–2.04) | 0.66 | 14 | 11 |
| A/A | 2 (1) | 0 (0) | N/A | 0.14 | 0.5 | 0.3 |
| G | 285 (91) | 469 (93) | 93 | 94 | ||
| A | 27 (9) | 33 (7) | 1.34 (0.79–2.27) | 0.33 | 7 | 6 |
| XRCC1 codon 399 G>A Arg/Gln | ||||||
| G/G | 96 (62) | 135 (54) | 57 | 54 | ||
| G/A | 50 (32) | 99 (39) | 0.70 (0.46–1.08 | 0.13 | 36 | 37 |
| A/A | 10 (6) | 17 (7) | 0.82 (0.36–1.86) | 0.68 | 7 | 9 |
| G | 244 (78) | 369 (74) | 75 | 70 | ||
| A | 70 (22) | 133 (26) | 0.79 (0.57–1.11) | 0.18 | 25 | 30 |
| XRCC3 codon 241 C>T Thr/Met | ||||||
| C/C | 51 (33) | 101 (40) | 37 | 44 | ||
| C/T | 86 (55) | 106 (42) | 1.60 (1.03–2.50) | 0.03 | 47 | 22 |
| T/T | 19 (12) | 44 (18) | 0.85 (0.45–1.61) | 0.64 | 16 | 34 |
| C | 188 (60) | 308 (61) | 61 | 56 | ||
| T | 124 (40) | 194 (39) | 1.05 (0.78–1.40) | 0.77 | 39 | 44 |
| Ku80 untranslated mRNA2790 A/G | ||||||
| A/A | 119 (76) | 164 (65) | 70 | 70 | ||
| A/G | 32 (21) | 79 (32) | 1.79 (1.11–2.88 | 0.01 | 27 | 26 |
| G/G | 5 (3) | 8 (3) | 1.16 (0.37–3.64) | 1 | 3 | 4 |
| A | 270 (87) | 407 (81) | 83 | 85 | ||
| G | 42 (13) | 95 (19) | 1.5 (1.01–2.23) | 0.04 | 17 | 15 |
| DNA Ligase IV codon 9 C/T Thr/lle | ||||||
| C/C | 132 (85) | 216 (86) | 85 | 71 | ||
| C/T | 24 (15) | 31 (12) | 1.27 (0.71–2.25) | 0.46 | 14 | 26 |
| T/T | 0 (0) | 4 (2) | N/A | 0.3 | 1 | 3 |
| C | 288 (92) | 463 (92) | 92 | 85 | ||
| T | 24 (8) | 39 (8) | 0.99 (0.58–1.68) | 1 | 8 | 15 |
| DNA-PKcs codon 3434 A/G Ile/Thr | ||||||
| A/A | 135 (87) | 212 (85.5) | 85.3 | 69 | ||
| A/G | 21 (13) | 38 (15) | 0.87 (0.49–1.54) | 0.67 | 14.5 | 27 |
| G/G | 0 (0) | 1 (0.5) | N/A | 1 | 0.2 | 4 |
| A | 291 (93) | 462 (92) | 92.5 | 82 | ||
| G | 21 (7) | 40 (8) | 0.83 (0.48–1.44) | 0.58 | 7.5 | 18 |
| TGFβ1 codon 10 T>C Leu/Pro | ||||||
| T/T | 51 (33) | 83 (33) | 33 | 57 | ||
| T/C | 67 (43) | 120 (48) | 0.91 (0.57–1.44) | 0.72 | 46 | 31 |
| C/C | 38 (24) | 48 (19) | 1.29 (0.74–2.23) | 0.4 | 21 | 12 |
| T | 169 (54) | 286 (57) | 56 | 79 | ||
| C | 143 (46) | 216 (43) | 1.12 (0.84–1.49) | 0.47 | 44 | 21 |
| MDM2 promoter309 T/G | ||||||
| T/T | 69 (44) | 67 (27) | 33 | N/A | ||
| T/G | 61 (39) | 120 (48) | 0.49 (0.31–0.79) | 0.003 | 45 | N/A |
| G/G | 26 (17) | 64 (25) | 0.39 (0.22–0.69) | 0.001 | 22 | N/A |
| T | 199 (64) | 254 (51) | 56 | N/A | ||
| G | 113 (36) | 248 (49) | 0.58 (0.43–0.78) | 0.0003 | 44 | N/A |
a
Manually calculated from NCBI Web site for each SNP.
N/A, not applicable.