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Table 2 The effect of methylation of every of the 22 CpGs on 5-year OS time

From: Large-scale analysis of DFNA5 methylation reveals its potential as biomarker for breast cancer

CpG

Genomic coordinate (GRCh37)

All breast adenocarcinomas

Ductal adenocarcinomas

Lobular adenocarcinomas

Regression coefficient

S.E.

P value

Regression coefficient

S.E.

P value

Regression coefficient

S.E.

P value

CpG17790129

24738572

5.1

1.9

8.2 × 10−3 *

6.0

2.5

0.019 *

2.3

3.8

0.54

CpG14205998

24748668

5.1

2.1

0.015 *

4.9

2.1

0.023 *

13.9

11.9

0.24

CpG04317854

24762562

1.8

1.3

0.16

2.6

1.4

0.064

− 2.6

3.5

0.46

CpG12922093

24767644

3.1

1.2

0.012 *

3.8

1.4

6.2 × 10−3 *

− 1.9

4.2

0.66

CpG17569154

24781545

3.0

1.2

0.012 *

3.6

1.3

6.3 × 10−3 *

− 2.3

4.4

0.61

CpG19260663

24791121

5.3

1.9

4.2 × 10−3 *

5.7

2.0

5.5 × 10−3 *

7.5

6.3

0.23

CpG09333471

24796355

2.5

1.3

0.059

1.7

1.4

0.22

11.4

6.8

0.093

CpG00473134

24796494

0.81

1.4

0.57

0.78

1.6

0.62

4.3

4.8

0.37

CpG03995857

24796553

− 0.19

1.0

0.85

− 0.75

1.1

0.49

7.4

5.2

0.16

CpG07320646

24796981

− 0.49

0.84

0.55

− 1.3

1.0

0.22

7.0

5.3

0.19

CpG07293520

24797192

− 0.17

1.2

0.89

− 1.7

1.6

0.29

9.5

5.3

0.072

CpG04770504

24797363

− 1.3

1.2

0.27

− 2.4

1.4

0.098

11.7

8.8

0.18

CpG24805239

24797486

− 0.19

1.2

0.87

− 0.91

1.3

0.49

6.4

4.5

0.16

CpG01733570

24797656

0.97

1.0

0.34

0.77

1.0

0.44

3.9

3.9

0.32

CpG25723149

24797680

0.14

1.0

0.89

0.18

1.0

0.86

2.2

4.1

0.59

CpG22804000

24797691

− 0.092

1.1

0.93

0.087

1.1

0.94

0.51

3.9

0.90

CpG07504598

24797786

− 0.31

1.1

0.77

− 0.13

1.1

0.91

0.87

4.2

0.83

CpG15037663

24797835

− 0.21

1.1

0.85

− 0.086

1.1

0.94

3.4

4.8

0.48

CpG19706795

24797839

0.29

1.2

0.80

0.67

1.2

0.58

0.13

4.3

0.98

CpG20764575

24797884

− 0.77

1.1

0.46

− 0.60

1.1

0.57

0.84

5.0

0.87

CpG06301139

24798175

4.2

2.3

0.064

5.0

2.6

0.052

2.9

5.9

0.63

CpG26712096

24798855

2.4

1.2

0.053

2.7

1.3

0.036 *

3.9

4.2

0.35

  1. For each of the 22 CpGs, the effect size (= regression coefficient) with standard error (S.E.) and the p value (likelihood ratio test) are reported for the effect on 5-year OS time in all breast adenocarcinoma patients, only the ductal, or only the lobular carcinoma patients. CpG17790129–CpG19260663 are located in the gene body, CpG09333471–CpG20764575 are located in the putative gene promoter, and the last two CpGs, CpG06301139 and CpG26712096, are located upstream from the putative gene promoter
  2. *Significant p values
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Clinical Epigenetics

ISSN: 1868-7083

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