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Table 1 Genotype and allele frequencies of rs4685 (SF3B1), rs12366395 (TBX3), rs72758040 (MAP3K1), rs8853 (TBX3), and rs1061651 (TBX3) in BRCA1/2-negative breast cancer cases and controls

From: Heritable genomic diversity in breast cancer driver genes and associations with risk in a Chilean population

   All BC cases (n = 486) Families with ≥ 2 BC and/or OC cases (n = 308) Families with a single case, diagnosis at ≤ 50 years of age (n = 178)
Genotype or allele Controls (%) (n = 1258) BC cases (%) OR [95% CI] p-valuea BC cases (%) OR [95% CI] p-valuea BC cases (%) OR [95% CI] p-valuea
rs4685 (SF3B1)
 C/C 504 (40.1) 213 (43.8) (ref.) 133 (43.2) (ref.) 80 (44.9) (ref.)
 C/T 560 (44.5) 213 (43.8) 0.9 [0.7–1.1] 0.35 139 (45.1) 0.9 [0.7–1.2] 0.68 74 (41.6) 0.8 [0.5–1.1] 0.30
 T/T 194 (15.4) 60 (12.4) 0.7 [0.5–1.0] 0.07 36 (11.7) 0.7 [0.4–1.0] 0.09 24 (13.5) 0.7 [0.4–1.2] 0.34
 C/T + T/T 754 (59.9) 273 (56.2) 0.8 [0.6–1.0] 0.15 175 (56.8) 0.8 [0.6–1.1] 0.33 98 (55.1) 0.8 [0.5–1.1] 0.22
 Allele C 1568 (62.3) 639 (65.7) (ref.) 405 (65.7) (ref.) 234 (65.7) (ref.)
 Allele T 948 (37.7) 333 (34.3) 0.8 [0.7–1.0] 0.06 211 (34.3) 0.8 [0.7–1.0] 0.12 122 (34.3) 0.8 [0.6–1.0] 0.23
rs12366395 (TBX3)
 A/A 989 (78.6) 355 (73.0) (ref.) 220 (71.4) (ref.) 135 (75.8) (ref.)
 A/G 252 (20.0) 124 (25.5) 1.3 [1.0–1.7] 0.01 82 (26.6) 1.4 [1.0–1.9] 0.01 42 (23.6) 1.2 [0.8–1.7] 0.3
 G/G 17 (1.4) 7 (1.4) 1.1 [0.4–2.7] 0.8 6 (1.9) 1.5 [0.6–4.0] 0.4 1 (0.6) 0.4 [0.05–3.2] 0.7
 A/G + G/G 269 (21.4) 131 (27.0) 1.3 [1.0–1.7] 0.01 88 (28.6) 1.4 [1.1–1.9] 0.008 43 (24.2) 1.1 [0.8–1.6] 0.4
 Allele A 2230 (88.6) 834 (85.8) (ref.) 522 (84.7) (ref.) 312 (87.6) (ref.)
 Allele G 286(11.4) 138 (14.2) 1.2 [1.0–1.6] 0.02 94 (15.3) 1.4 [1.0–1.8] 0.009 44 (12.4) 1.1 [0.7–1.5] 0.6
rs72758040 (MAP3K1)
 G/G 866 (68.8) 317 (65.4) (ref.) 194 (63.3) (ref.) 123 (69.1) (ref.)
 G/C 307 (24.4) 119 (24.5) 1.0 [0.8–1.3] 0.65 76 (24.7) 1.1 [0.8–1.4] 0.54 43 (24.2) 0.9 [0.6–1.4] 1.0
 C/C 85 (6.8) 50 (10.1) 1.6 [1.1–2.3] 0.01 38 (12.0) 1.9 [1.3–3.0] 0.001 12 (6.7) 0.9 [0.5–1.8] 1.0
 G/C + C/C 392 (31.2) 168 (34.6) 1.1 [0.9–1.4] 0.16 113 (36.7) 1.2 [0.9–1.6] 0.06 55 (30.9) 0.9 [0.7–1.3] 1.0
 Allele G 2039 (81.0) 755 (77.7) (ref.) 466 (75.6) (ref.) - 289 (81.2) (ref.)
 Allele C 477 (19.0) 217 (22.3) 1.2 [1.0–1.4] 0.02 150 (24.4) 1.3 [1.1–1.6] 0.003 67 (18.8) 0.9 [0.7–1.3] 0.9
rs8853 (TBX3)
 T/T 512 (40.7) 195 (40.1) (ref.) 125 (40.6) (ref.) 70 (39.3) (ref.)
 T/C 563 (44.8) 217 (44.7) 1.0 [0.8–1.2] 0.95 132 (42.9) 0.9 [0.7–1.2] 0.78 85 (47.8) 1.1 [0.7–1.5] 0.60
 C/C 183 (14.5) 74 (15.2) 1.0 [0.7–1.4] 0.74 51 (16.5) 1.1 [0.7–1.6] 0.50 23 (12.9) 0.9 [0.5–1.5] 0.80
 T/C + C/C 746 (59.3) 291 (59.9) 1.0 [0.8–1.2] 0.87 183 (59.4) 1.0 [0.7–1.2] 1.00 108 (60.7) 1.0 [0.7–1.4] 0.74
 Allele T 1587 (63.1) 607 (62.4) (ref.) 382 (62.0) (ref.) 225 (63.2) (ref.)
 Allele C 929 (36.9) 365 (37.6) 1.0 [0.8–1.1] 0.76 234 (38.0) 1.0 [0.8–1.2] 0.65 131 (36.8) 0.9 [0.7–1.2] 0.99
rs1061651 (TBX3)
 T/T 414 (32.9) 154 (31.7) (ref.) 98 (31.8) (ref.) - 56 (31.5) (ref.)
 T/C 596 (47.4) 240 (49.4) 1.0 [0.8–1.3] 0.54 153 (49.7) 1.0 [0.8–1.4] 0.61 87 (48.9) 1.0 [0.7–1.5] 0.71
 C/C 248 (19.7) 92 (18.9) 0.9 [0.7–1.3] 1.00 57 (18.5) 0.9 [0.6–1.3] 0.92 35 (19.7) 1.0 [0.6–1.6] 0.90
 T/C + C/C 844 (67.1) 332 (68.3) 1.0 [0.8–1.3] 0.64 210 (68.2) 1.0 [0.8–1.3] 0.73 122 (68.5) 1.0 [0.7–1.4] 0.73
 Allele T 1424 (56.6) 548 (56.4) (ref.) 349 (56.7) (ref.) 199 (55.9) (ref.)
 Allele C 1092 (43.4) 424 (43.6) 1.0 [0.8–1.1] 0.93 267 (43.3) 0.9 [0.8–1.1] 0.98 157 (44.1) 1.0 [0.8–1.2] 0.84
  1. BC breast cancer, OC ovarian cancer, OR odds ratio, CI confidence interval, Ref reference
  2. aFisher’s exact test; bold values are statistically significant (p < 0.05)