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Table 1 Comparison of clinical characteristics between patients with and without DNA-repair pathway gene mutation

From: DrABC: deep learning accurately predicts germline pathogenic mutation status in breast cancer patients based on phenotype data

Clinical characteristics Without GPVs (n = 2347) All CPGs (n = 332) BRCA1 carriers (n = 131) BRCA2 carriers (n = 132) Other HRR-related genes (n = 43) Other CPGs (n = 26) P 1 P 2 P 3 P 4 P 5
Age at enrollment a 45.2 ± 8.8 42.1 ± 8.4 40.7 ± 8.6 43.1 ± 7.9 44.0 ± 9.1 41.2 ± 7.7 2.3 × 10−9 1.2 × 10−8 7.4 × 10−4 0.38 0.02
Age of onset a 43.4 ± 9.1 40.2 ± 8.3 39.1 ± 8.4 40.8 ± 8.0 41.2 ± 9.1 40.5 ± 7.6 5.7 × 10−10 8.6 × 10−8 1.2 × 10−3 0.11 0.11
≤40 years b 885 (37.7%) 186 (56.0%) 79 (60.3%) 67 (50.8%) 25 (58.1%) 15 (57.7%) 3.5 × 10−10 4.6 × 10−7 3.2 × 10−3 0.01 0.04
>  40 years b 1462 (62.3%) 146 (44.0%) 52 (39.7%) 65 (49.2%) 18 (41.9%) 11 (42.3%)      
Personal history b
 Any cancer 113 (4.8%) 39 (11.8%) 16 (12.2%) 18 (13.6%) 3 (7.0%) 2 (7.7%) 5 × 10−6 9.5 × 10−4 1.3 × 10−4 0.46 0.36
 Previous breast cancer 47 (2.0%) 26 (7.8%) 14 (10.7%) 10 (7.6%) 1 (2.3%) 1 (3.9%) 1.8 × 10−7 2.0 × 10−6 6.6 × 10−4 0.59 0.41
 Ovarian cancer 8 (0.3%) 4 (1.2%) 1 (0.8%) 3 (2.3%) 0 (0%) 0 (0%) 0.05 0.39 0.02 1 1
Family history b
 Any cancer 726 (30.9%) 183 (55.1%) 85 (64.9%) 71 (53.8%) 15 (34.9%) 12 (46.2%) 3.4 × 10−17 1.6 × 10−14 1.5 × 10−7 0.62 0.13
 Breast cancer 254 (10.8%) 108 (32.5%) 54 (41.2%) 43 (32.6%) 7 (16.3%) 4 (15.4%) 3.2 × 10−22 8.4 × 10−18 9.5 × 10−11 0.32 0.52
 Ovarian cancer 18 (0.8%) 21 (6.3%) 19 (14.5%) 1 (0.8%) 0 (0%) 1 (3.9%) 3.8 × 10−10 1.2 × 10−15 1 1 0.19
 Pancreas cancer 34 (1.5%) 11 (3.3%) 4 (3.1%) 2 (1.5%) 4 (9.3%) 1 (3.9%) 0.02 0.14 0.72 4.3 × 10−3 0.32
 Prostate cancer 10 (0.4%) 0 (0%) 0 (0%) 0 (0%) 0 (0%) 0 (0%) 0.62 1 1 1 1
 Esophageal cancer 82 (3.5%) 13 (3.9%) 7 (5.3%) 3 (2.3%) 2 (4.7%) 1 (3.9%) 0.64 0.23 0.62 0.66 0.61
 Laryngeal cancer 12 (0.5%) 5 (1.5%) 2 (1.5%) 2 (1.5%) 0 (0%) 1 (3.9%) 0.05 0.17 0.17 1 0.13
 Leukemia 13 (0.6%) 5 (1.5%) 1 (0.8%) 3 (2.3%) 0 (0%) 1 (3.9%) 0.06 0.53 0.05 1 0.14
 Male breast cancer 2 (0.1%) 4 (1.2%) 0 (0%) 4 (3.0%) 0 (0%) 0 (0%) 2.8 × 103 1 1.1 × 10−4 1 1
Tumor size b
 ≤ 2 cm 1099 (46.8%) 146 (44.0%) 51 (38.9%) 62 (47.0%) 18 (41.9%) 15 (57.7%) 0.16 0.06 0.63 0.41 0.28
 > 2 cm 899 (38.3%) 143 (43.1%) 60 (45.8%) 56 (42.4%) 20 (46.5%) 7 (27.0%)      
Histology b
 IDC 1825 (77.8%) 295 (88.9%) 122 (93.1%) 114 (86.4%) 38 (88.4%) 21 (80.8%) 1 × 10−6 5 × 10−6 0.02 0.14 0.82
 DCIS 184 (7.8%) 11 (3.3%) 0 (0%) 7 (5.3%) 2 (4.7%) 2 (7.7%) 2.1 × 10−3 4.9 × 10−5 0.40 0.77 1
 Lobular 45 (1.9%) 6 (1.8%) 1 (0.8%) 3 (2.3%) 1 (2.3%) 1 (3.9%) 1 0.51 0.74 0.57 0.40
 Mucinous 45 (1.9%) 3 (0.9%) 0 (0%) 2 (1.5%) 1 (2.3%) 0 (0%) 0.27 0.17 1 0.57 1
 Medullary 11 (0.5%) 4 (1.2%) 2 (1.5%) 2 (1.5%) 0 (0%) 0 (0%) 0.10 0.15 0.15 1 1
 Other c 34 (1.5%) 4 (1.2%) 2 (1.5%) 1 (0.8%) 0 (0%) 1 (3.9%) 1 0.72 1 1 0.32
Grade b
 I 139 (5.9%) 2 (0.6%) 0 (0%) 2 (1.5%) 0 (0%) 0 (0%) 2 × 10−6 6.8 × 10−4 0.03 0.18 0.40
 II 1004 (42.8%) 129 (38.9%) 26 (19.9%) 67 (50.8%) 26 (60.5%) 10 (38.5%) 0.19 8.4 × 10−8 0.09 0.03 0.70
 III 587 (25.0%) 134 (40.4%) 85 (64.9%) 35 (26.5%) 8 (18.6%) 6 (23.1%) 1.5 × 10−8 1.5 × 10−20 0.68 0.38 1
ER status b
 Positive 1592 (67.8%) 190 (57.2%) 34 (26.0%) 107 (81.1%) 30 (69.8%) 19 (73.1%) 1 × 10−6 4.1 × 10−25 0.01 0.86 0.82
 Negative 612 (26.1%) 134 (40.4%) 94 (71.8%) 22 (16.7%) 12 (27.9%) 6 (23.1%)      
PR status b
 Positive 1571 (66.9%) 192 (57.8%) 35 (26.7%) 107 (81.1%) 32 (74.4%) 18 (69.2%) 2.3 × 10−5 2.6 × 10−23 2.3 × 10−3 0.61 1
 Negative 631 (26.9%) 131 (39.5%) 93 (71.0%) 21 (15.9%) 10 (23.3%) 7 (26.9%)      
AR status b
 Positive 710 (30.3%) 69 (20. 8%) 15 (11.5%) 33 (25.0%) 10 (23.3%) 11 (42.3%) 2.8 × 10−14 4.6 × 10−21 0.19 0.02 1
 Negative 175 (7.5%) 73 (22.0%) 50 (38.2%) 13 (9.9%) 8 (18.6%) 2 (7.7%)      
HER2 status b
 Positive 507 (21.6%) 15 (4.5%) 2 (1.5%) 6 (4.6%) 0 (0%) 7 (26.9%) 8.1 × 10−17 4.2 × 10−11 1.1 × 10−7 4.3 × 10−5 0.48
 Negative 1317 (56.1%) 277 (83.4%) 120 (91.6%) 103 (78.0%) 37 (86.1%) 17 (65.4%) 2.8 × 10−23 3.7 × 10−18 4.5 × 10−7 6.3 × 10−5 0.43
 Uncertain 342 (14.6%) 27 (8.1%) 3 (2.3%) 18 (13.6%) 4 (9.3%) 2 (7.7%) 1.2 × 10−3 6 × 10−6 0.90 0.51 0.57
 TNBC b 303 (12.9%) 109 (32.8%) 82 (62.6%) 15 (11.4%) 8 (18.6%) 4 (15.4%) 9.5 × 10−18 6.8 × 10−37 0.69 0.25 0.77
Ki67 b
 ≤ 30% 1254 (53.4%) 134 (40.4%) 21 (16.0%) 74 (56.1%) 23 (53.5%) 16 (61.5%) 1.0 × 10−7 1.0 × 10−19 0.85 0.87 0.54
 > 30% 852 (36.3%) 175 (52.7%) 98 (74.8%) 52 (39.4%) 17 (39.5%) 8 (30.8%)      
EGFR b
 Positive 467 (19.9%) 110 (33.1%) 72 (55.0%) 23 (17.4%) 9 (20.9%) 6 (23.1%) 2.5 × 10−5 2.4 × 10−17 0.11 0.85 0.79
 Negative 1026 (43.7%) 132 (39.8%) 24 (18.3%) 75 (56.8%) 22 (51.2%) 11 (42.3%)      
CK5/6 b
 Positive 309 (13.2%) 90 (27.1%) 61 (46.6%) 16 (12.1%) 10 (23.3%) 3 (11.5%) 9.0 × 10−8 1.1 × 10−17 0.51 0.19 0.78
 Negative 1382 (58.9%) 181 (54.5%) 46 (35.1%) 89 (67.4%) 26 (60.5%) 20 (76.9%)      
P53 b
 Gain-of-function 605 (25.8%) 100 (30.1%) 46 (35.1%) 39 (29.6%) 10 (23.3%) 5 (19.2%) 0.10 0.02 0.36 0.86 0.65
 Loss-of-function 227 (9.7%) 49 (14.8%) 33 (25.2%) 6 (4.6%) 4 (9.3%) 6 (23.1%) 6.7 × 10−3 9.5 × 10−7 0.05 1 0.04
 Wildtype 629 (26.8%) 103 (31.0%) 21 (16.0%) 55 (41. 7%) 20 (46.5%) 7 (26.9%) 0.11 5.7 × 10−3 4.1 × 10−4 0.01 1
 Bilateral breast cancer b 52 (2.2%) 28 (8.4%) 15 (11.5%) 11 (8.3%) 1 (2.3%) 1 (3.9%) 9.2 × 10−8 1.0 × 10−6 3.7 × 10−4 0.62 0.45
Lymph nodes status b
 Positive 892 (38.0%) 153 (46.1%) 43 (32.8%) 75 (56.8%) 21 (48.8%) 14 (53.9%) 0.01 0.13 4 × 10−6 0.13 0.05
 Negative 1151 (49.0%) 143 (43.1%) 76 (58.0%) 44 (33.3%) 16 (37.2%) 7 (26.9%)      
  1. aMean ± SD, year, Student’s T test
  2. bNo. (%), Pearson’s chi-square test or Fisher’s exact test
  3. cOthers include metaplastic cancer, sieve cancer, Paget’s disease, micropapillary cancer, secretory cancer, tubule cancer
  4. dP < 0.05 is considered significant. P1 non-carriers vs. all CPGs carriers, P2 non-carriers vs. BRCA1 carriers, P3 non-carriers vs. BRCA2 carriers, P4 non-carriers vs. other HRR-related genes carriers, P5 non-carriers vs. other CPGs carriers
  5. eNumbers of patients with each unknown characteristic were not shown
  6. Abbreviation: GPV germline pathogenic variant, CPG cancer predisposition gene, HRR homologous recombinational repair