Table 3 SNPs associated with clinico-pathological features
Gene/SNP | Genotype | Significant association | No. of patients Group 1(%) | No. of patients Group 2(%) | OR (95 % CI) | P-value | Significant association | No. of patients Group 1(%) | No. of patients Group 2(%) | OR (95 % CI) | P-value |
|---|---|---|---|---|---|---|---|---|---|---|---|
APOBEC3B | Tumor size | ≤2 cm | >2 cm | ||||||||
rs8142462 | CC | 68 (87.18) | 105 (76.09) | 1.00 | |||||||
TC | 8 (10.26) | 32 (23.19) | 2.59 (1.13-5.96) | 0.0300 | |||||||
TT | 2 (2.56) | 1 (0.72) | 0.32 (0.03-3.64) | 0.3600 | |||||||
TC + TT | 10 (12.82) | 33 (23.91) | 2.14 (0.99-4.62) | 0.0500 | |||||||
Overall | 0.0500 | ||||||||||
APOBEC3B | Estrogen receptor/Progesterone receptors | ER+/PR+ | ER-/PR- | Estrogen receptor | ER+ | ER- | |||||
rs28401571 | CC | 48 (43.24) | 21 (39.62) | 1.00 | 59 (43.38) | 30 (41.67) | 1.00 | ||||
CT | 49 (44.14) | 16 (30.19) | 0.75 (0.35-1.60) | 0.4500 | 62 (45.59) | 22 (30.56) | 0.70 (0.36-1.34) | 0.2800 | |||
TT | 14 (12.61) | 16 (30.19) | 2.61 (1.08-6.31) | 0.0300 | 15 (11.03) | 20 (27.78) | 2.62 (1.18-5.84) | 0.0200 | |||
CT + TT | 63 (56.76) | 32 (60.38) | 1.16 (0.60-2.26) | 0.6600 | 77 (56.62) | 42 (58.33) | 1.07 (0.60-1.91) | 0.8100 | |||
Overall | 0.0200 | 0.0100 | |||||||||
APOBEC3B | Estrogen receptor/Progesterone receptors | ER+/PR+ | ER-/PR- | ||||||||
rs2076111 | CC | 40 (36.04) | 11 (20.75) | 1.00 | |||||||
CT | 67 (60.36) | 41 (77.36) | 2.23 (1.03-4.82) | 0.0400 | |||||||
TT | 4 (3.60) | 1 (1.89) | 0.91 (0.09-8.98) | 0.9300 | |||||||
CT + TT | 71 (63.96) | 42 (79.25) | 2.15(1.00-4.64) | 0.0500 | |||||||
Overall | 0.1000 | ||||||||||
ATR | Tumor Size | ≤2 cm | >2 cm | Estrogen receptor/Progesterone receptors | ER+/PR+ | ER+/PR- | |||||
rs2227928 | GG | 33 (42.31) | 40 (28.99) | 1.00 | 33 (29.73) | 13 (52.00) | 1.00 | ||||
AG | 34 (43.59) | 71 (51.45) | 1.72 (0.93-3.19) | 0.0800 | 58 (52.25) | 10 (40.00) | 0.44 (0.17-1.11) | 0.0800 | |||
AA | 11 (14.10) | 27 (19.57) | 2.02 (0.88-4.69) | 0.0900 | 20 (18.02) | 2 (8.00) | 0.25 (0.05-1.24) | 0.0900 | |||
AG + AA | 45 (57.69) | 98 (71.01) | 1.80 (1.01-3.21) | 0.0400 | 78 (70.27) | 12 (48.00) | 0.39 (0.16-0.95) | 0.0300 | |||
Overall | 0.1300 | 0.0900 | |||||||||
MLL2 | Tumor Size | ≤2 cm | >2 cm | Histologic grade | 1 + 2 | 3 | |||||
rs11614738 | GG | 26 (33.33) | 61 (44.20) | 1.00 | 18 (30.51) | 69 (46.31) | 1.00 | ||||
CG | 37 (47.44) | 64 (46.38) | 0.74 (0.40-1.36) | 0.3200 | 35 (59.32) | 59 (39.60) | 0.44 (0.23-0.86) | 0.0100 | |||
CC | 15 (19.23) | 13 (9.42) | 0.37 (0.15-0.88) | 0.0200 | 6 (10.17) | 21 (14.09) | 0.91 (0.32-2.60) | 0.8600 | |||
CG + CC | 52 (66.67) | 77 (55.80) | 0.63 (0.35-1.13) | 0.1100 | 41 (69.49) | 80 (53.69) | 0.51 (0.27-0.97) | 0.0300 | |||
Overall | 0.0800 | 0.0300 | |||||||||
SMAD4 | Histologic grade | 1 + 2 | 3 | ||||||||
rs12456284 | AA | 36 (61.02) | 99 (66.44) | 1.00 | |||||||
AG | 18 (30.51) | 47 (31.54) | 0.95 (0.49-1.84) | 0.8700 | |||||||
GG | 5 (8.47) | 3 (2.01) | 0.22 (0.05-0.96) | 0.0400 | |||||||
AG + GG | 23 (38.98) | 50 (33.56) | 0.79 (0.42-1.48) | 0.4600 | |||||||
Overall | 0.1300 | ||||||||||
SMAD4 | Tumor Size | ≤2 cm | >2 cm | Estrogen receptor/Progesterone receptors | ER+/PR+ | ER+/PR- | |||||
rs3819122 | AA | 22 (28.21) | 64 (46.38) | 1.00 | 43 (38.74) | 15 (60.00) | 1.00 | ||||
AC | 45 (57.69) | 52 (37.68) | 0.40 (0.21-0.74) | 0.0030 | 48 (43.24) | 7 (28.00) | 0.42 (0.16-1.12) | 0.0800 | |||
CC | 11 (14.10) | 22 (15.94) | 0.69 (0.29-1.64) | 0.3900 | 20 (18.02) | 3 (12.00) | 0.43 (0.11-1.66) | 0.2100 | |||
AC + CC | 56 (71.79) | 74 (53.62) | 0.45 (0.25-0.82) | 0.0090 | 68 (61.26) | 10 (40.00) | 0.42 (0.17-1.02) | 0.0500 | |||
Overall | 0.0100 | 0.1600 | |||||||||
TBX3 | Histologic grade | 1 + 2 | 3 | ||||||||
rs3759173 | GG | 11 (18.64) | 47 (31.54) | 1.00 | |||||||
GT | 34 (57.63) | 69 (46.31) | 0.47 (0.22-1.03) | 0.0500 | |||||||
TT | 14 (23.73) | 33 (22.15) | 0.55 (0.22-1.37) | 0.1900 | |||||||
GT + TT | 48 (81.36) | 102 (68.46) | 0.50 (0.24-1.04) | 0.0600 | |||||||
Overall | 0.1600 | ||||||||||
TBX3 | Regional lymph node met | N- | N+ | ||||||||
rs8853 | CC | 67 (50.76) | 33 (38.37) | 1.00 | |||||||
CT | 53 (40.15) | 49 (56.98) | 1.88 (1.06-3.32) | 0.0300 | |||||||
TT | 12 (9.09) | 4 (4.65) | 0.68 (0.20-2.26) | 0.5200 | |||||||
CT + TT | 65 (49.24) | 53 (61.63) | 1.66 (0.95-2.88) | 0.0700 | |||||||
Overall | 0.0400 | ||||||||||
TTN | Regional lymph node met | N- | N+ | ||||||||
rs2303838 | CC | 87 (65.91) | 50 (58.14) | 1.00 | |||||||
CT | 42 (31.82) | 29 (33.72) | 1.20 (0.67-2.16) | 0.5400 | |||||||
TT | 3 (2.27) | 7 (8.14) | 4.06 (1.00-16.4) | 0.0400 | |||||||
CT + TT | 45 (34.09) | 36 (41.86) | 1.39 (0.80-2.44) | 0.2400 | |||||||
Overall | 0.1300 | ||||||||||
TTN | Estrogen receptor | ER+ | ER- | Estrogen receptor/Progesterone receptors | ER+/PR+ | ER-/PR- | |||||
rs2244492 | CC | 36 (26.47) | 32 (44.44) | 1.00 | 31 (27.93) | 23 (43.40) | 1.00 | ||||
CT | 77 (56.62) | 32 (44.44) | 0.47 (0.25-0.88) | 0.0100 | 63 (56.76) | 25 (47.17) | 0.53 (0.26-1.09) | 0.0800 | |||
TT | 23 (16.91) | 8 (11.11) | 0.39 (0.15-1.00) | 0.0400 | 17 (15.32) | 5 (9.43) | 0.40 (0.13-1.23) | 0.1000 | |||
CT + TT | 100 (73.53) | 40 (55.56) | 0.45 (0.25-0.82) | 0.0090 | 80 (72.07) | 30 (56.60) | 0.51 (0.26-1.00) | 0.0500 | |||
Overall | 0.0300 | 0.1300 | |||||||||
TTN | Progesterone receptor | PR+ | PR- | Estrogen receptor/Progesterone receptors | ER+/PR+ | ER-/PR- | |||||
rs12465459 | CC | 87 (66.92) | 40 (51.28) | 1.00 | 74 (66.67) | 27 (50.94) | 1.00 | ||||
CT | 39 (30.00) | 36 (46.15) | 2.01 (1.12-3.61) | 0.0200 | 34 (30.63) | 24 (45.28) | 1.93 (0.98-3.83) | 0.0500 | |||
TT | 4 (3.08) | 2 (2.56) | 1.09 (0.19-6.18) | 0.9200 | 3 (2.70) | 2 (3.77) | 1.83 (0.29-11.54) | 0.5200 | |||
CT + TT | 43 (33.08) | 38 (48.72) | 1.92 (1.08-3.42) | 0.0200 | 37 (33.33) | 26 (49.06) | 1.93 (0.99-3.75) | 0.0500 | |||
Overall | 0.0600 | 0.1500 | |||||||||
TTN | Progesterone receptor | PR+ | PR- | Regional lymph node met | N- | N+ | |||||
rs12463674 | AA | 70 (53.85) | 51 (65.38) | 1.00 | 71 (53.79) | 56 (65.12) | 1.00 | ||||
AG | 56 (43.08) | 22 (28.21) | 0.54 (0.29-0.99) | 0.0400 | 56 (42.42) | 25 (29.07) | 0.57 (0.31-1.02) | 0.0500 | |||
GG | 4 (3.08) | 5 (6.41) | 1.72 (0.44-6.71) | 0.4300 | 5 (3.79) | 5 (5.81) | 1.27 (0.35-4.60) | 0.7100 | |||
AG + GG | 60 (46.15) | 27 (34.62) | 0.62 (0.35-1.10) | 0.1000 | 61 (46.21) | 30 (34.88) | 0.62 (0.36-1.09) | 0.0900 | |||
Overall | 0.0700 | 0.1300 | |||||||||
Histologic grade | 1 + 2 | 3 | Estrogen receptor/Progesterone receptors | ER+/PR+ | ER-/PR+ | ||||||
34 (57.63) | 88 (59.06) | 1.00 | 64 (57.66) | 6 (31.58) | 1.00 | ||||||
19 (32.20) | 58 (38.93) | 1.18 (0.61-2.26) | 0.6100 | 44 (39.64) | 12 (63.16) | 2.91 (1.02-8.33) | 0.0400 | ||||
6 (10.17) | 3 (2.01) | 0.19 0.05-0.82) | 0.0200 | 3 (2.70) | 1 (5.26) | 3.56 (0.32-39.70) | 0.3000 | ||||
25 (42.37) | 61 (40.94) | 0.94 (0.51-1.74) | 0.8400 | 47 (42.34) | 13 (68.42) | 2.95 (1.04-8.33) | 0.0400 | ||||
0.0500 | 0.1200 |