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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 × 10−3

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