Table 3.
Promoter and intronic sequence variations of the NBN gene in French Canadian breast cancer cases and healthy controls.
| SNP | SNP ID1 (dbSNP ID) |
Location | Series (No.) | MAF2 | Common homozygote No. (expected)3 | Heterozygote No. (expected)3 | Rare homozygote No. (expected)3 | HWE p-value | OR (95% CI)4 | Reported MAF in Caucasian |
|---|---|---|---|---|---|---|---|---|---|---|
| 10 | c.-110-242delAGTA | Promoter | Cases (97) | 0.082 | 81 (81.66) | 16 (14.68) | 0 (0.66) | 0.38 | 3.4 | |
| (rs36226237) | Controls (72) | 0.028 | 68 (68.06) | 4 (3.89) | 0 (0.06) | 0.81 | (1.1–10.5) | |||
| 11 | c.702+149T/C | Intron 6 | Cases (97) | 0.082 | 83 (81.66) | 12 (14.68) | 2 (0.66) | 0.07 | 0.7 | 0.108–0.1175 |
| (rs3026271) | Controls (73) | 0.089 | 60 (60.58) | 13 (11.84) | 0 (0.58) | 0.40 | (0.3–1.6) | |||
| 12 | c.703-29C/T | Intron 6 | Cases (97) | 0.015 | 94 (94.02) | 3 (2.95) | 0 (0.02) | 0.88 | 1.1 | 0.0215 |
| (NA)6 | Controls (73) | 0.014 | 71 (71.01) | 2 (1.97) | 0 (0.01) | 0.91 | (0.2–7.0) | |||
| 13 | c.703-18G/A | Intron 6 | Cases (97) | 0.026 | 92 (92.06) | 5 (4.87) | 0 (0.06) | 0.79 | 3.9 | |
| (rs769418) | Controls (73) | 0.007 | 72 (72.00) | 1 (0.99) | 0 (0) | 0.95 | (0.4–34.2) | |||
| 14 | c.896+36G/A | Intron 7 | Cases (97) | 0.026 | 92 (92.06) | 5 (4.87) | 0 (0.06) | 0.79 | 3.9 | 0.021–0.055 |
| (rs1805826) | Controls (73) | 0.007 | 72 (72.00) | 1 (0.99) | 0 (0) | 0.95 | (0.4–34.2) | |||
| 15 | c.897-42G/C | Intron 7 | Cases (97) | 0.015 | 94 (94.02) | 3 (2.95) | 0 (0.02) | 0.76 | 0.4 | |
| (NA)6 | Controls (73) | 0.034 | 68 (68.09) | 5 (4.83) | 0 (0.09) | 0.76 | (0.1–1.9) | |||
| 16 | c.994+233G/A | Intron 8 | Cases (97) | 0.294 | 50 (48.37) | 37 (40.25) | 10 (8.37) | 0.43 | 0.7 | 0.285 |
| (rs6990969) | Controls (74) | 0.311 | 34 (35.15) | 34 (31.70) | 6 (7.15) | 0.53 | (0.4–1.4) | |||
| 17 | c.1124+18C/T | Intron 9 | Cases (97) | 0.278 | 52 (50.52) | 36 (38.97) | 9 (7.52) | 0.45 | 0.7 | 0.09–0.3065 |
| (rs2234744) | Controls (74) | 0.304 | 35 (35.84) | 33 (31.32) | 6 (6.84) | 0.64 | (0.4–1.4) | |||
| 18 | c.1124+91C/A | Intron 9 | Cases (97) | 0.273 | 53 (51.24) | 35 (38.52) | 9 (7.24) | 0.37 | 0.7 | 0.283–0.3065 |
| (rs1805818) | Controls (74) | 0.304 | 35 (35.84) | 33 (31.32) | 6 (6.84) | 0.64 | (0.4–1.3) | |||
| 19 | c.1125-79C/A | Intron 9 | Cases (97) | 0.284 | 52 (49.80) | 35 (39.41) | 10 (7.80) | 0.27 | 0.8 | 0.3235 |
| (rs1805786) | Controls (72) | 0.292 | 36 (36.13) | 30 (29.75) | 6 (6.13) | 0.94 | (0.4–1.5) | |||
| 20 | c.1915-7A/G | Intron 12 | Cases (97) | 0.284 | 52 (49.80) | 35 (39.41) | 10 (7.80) | 0.27 | 0.8 | 0.20–0.3125 |
| (rs2308962) | Controls (70) | 0.300 | 34 (34.30) | 30 (29.40) | 6 (6.30) | 0.86 | (0.4–1.5) | |||
| 21 | c.2071-30A/T | Intron 13 | Cases (97) | 0.284 | 52 (49.80) | 35 (39.41) | 10 (7.80) | 0.27 | 0.7 | |
| (rs3736639) | Controls (71) | 0.310 | 33 (33.82) | 32 (30.37) | 6 (6.82) | 0.65 | (0.4–1.3) | |||
| 22 | c.2234+86T/G | Intron 15 | Cases (97) | 0.010 | 95 (95.01) | 2 (1.98) | 0 (0.01) | 0.92 | 3.8 | |
| (NA) | Controls (72) | 0.000 | 72 (72.00) | 0 (0) | 0 (0) | 1.00 | (0.2–80.3) | |||
| 23 | c.2234+88C/G | Intron 15 | Cases (97) | 0.015 | 94 (94.02) | 3 (2.95) | 0 (0.02) | 0.88 | 0.4 | 0.017–0.0425 |
| (rs13312970) | Controls (71) | 0.035 | 66 (66.09) | 5 (4.82) | 0 (0.09) | 0.76 | (0.1–1.8) | |||
| 24 | c.2234+157A/G | Intron 15 | Cases (97) | 0.046 | 88 (88.21) | 9 (8.58) | 0 (0.21) | 0.63 | 2.3 | 0.000–0.0255 |
| (rs13312971) | Controls (71) | 0.021 | 68 (68.03) | 3 (2.94) | 0 (0.03) | 0.86 | (0.6–8.9) | |||
1 According to the nomenclature guidelines of the Human Genome Variation Society (reference sequence NM_002485.4), nucleotide number one being the A from the ATG codon. 2 Minor allele frequency 3 As expected under Hardy-Weinberg equilibrium 4 Odds ratios for comparison of heterozygotes versus common homozygotes 5 From NCBI dbSNP data. 6 No entry in NCBI dbSNP database, although reported in the literature.