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Table 3 SNPs associated with clinico-pathological features

From: Analysis of functional germline variants in APOBEC3 and driver genes on breast cancer risk in Moroccan study population

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
  1. OR odds ratio, CI confidence interval, SNP single nucleotide polymorphism, No total number