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Table 1 A summary of aberrant DNA methylation associated with outcome in breast cancer

From: Epigenome remodelling in breast cancer: insights from an early in vitro model of carcinogenesis

Gene symbol

Tissue type

Hyper/Hypo

Cohort size

Detection method

Association with prognosis

Pvalue

Hazard ratioa

Reference

ACADL

NR

Hyper

59 ductal carcinomas, 24 matched normal

IA/CoBRA

Reduced relapse-free survival

0.0001

 

[50]

BMP4

FF

Hyper

241 patients with breast cancer

MethyLight

Reduced time to distant metastasis

0.0002

 

[51]

BRCA1

FFPE

Hyper

536 tumors (Chinese patients)

MSP

Reduced disease-free survival

0.045

1.45

[52]

     

Reduced disease-specific survival

0.038

1.56

 
 

FF

Hyper

241 patients with breast cancer

MethyLight

Reduced time to distant metastasis

0.018

 

[51]

 

Serum

Hyper

105 tumors, 20 unmatched normal

MSP

Poor prognosis

0.002

6.4

[53]

 

FF

Hyper

82 primary breast cancer tissues (Tunisian cohort)

MSP

Five-year survival

0.016

 

[54]

BRCA1 or P16 or both

Serum

Hyper

105 tumors, 20 unmatched normal

MSP

Poor prognosis

0.002

10.7

[53]

C20ORF55

FF

Hyper

241 patients with breast cancer

MethyLight

Reduced time to distant metastasis

0.001

 

[51]

CDO1

FF

Hyper

163 tumors, 64 with distant metastasis

Q-BSSeq

Reduced time to distant metastasis

<0.0128

>3.5

[55]

     

Reduced metastasis-free survival

<0.0034

  

CIDEB

FF

Hyper

110 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.002

4.02

[56]

CST6

FFPE

Hyper

93 carcinomas, 10 carcinomas with adjacent normal, 10 fibroadenomas, and 11 normal

MSP

Reduced disease-free interval Reduced overall survival

0.004 0.001

 

[57]

     

Reduced disease-free interval

0.027

3.48

 
     

Reduced overall survival

0.004

9.19

 

DKK3

FF

Hyper

153 primary invasive cancers, 19 normal

MSP

Reduced overall survival

0.011

14.4

[58]

     

Reduced disease-free survival

0.047

2.5

 

ELK1

FF

Hyper

130 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.005

3.53

[56]

ESR2 (ER-B)

FF

Hyper

55 cancers

MSP

Increased incidence of relapse

0.016

 

[59]

FGF12

FF

Hyper

113 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.004

3.31

[56]

FGF4

FF

Hyper

241 patients with breast cancer

MethyLight

Reduced time to distant metastasis

0.029

 

[51]

FOXH1

FF

Hyper

129 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.00007

5.09

[56]

FOXL2

FF

Hyper

241 patients with breast cancer

MethyLight

Reduced time to distant metastasis

0.02

 

[51]

GSTP1

FF

Hyper

176 invasive tumors (Japanese cohort)

MSP

Reduced relapse-free survival

<0.01

 

[60]

     

Poor prognosis

<0.05

2.77

 
     

Poor prognosis

<0.01

7.13

 
 

FFPE

Hyper

974 primary in situ or invasive breast cancers

MethyLight

Increased breast cancer-specific mortality

NR

1.71

[61]

 

FFPE

Hyper

50 breast tumors

MSP

High Nottingham Prognostic Index

0.0017

 

[62]

HOXB13

FF

Hyper

57 ER-α+ tumors

QM-PCR

Reduced disease-free survival

0.029

3.25

[36]

ID4

FF

Hyper

171 tumors and match normal

MSP

Reduced recurrence-free survival

0.036

 

[63]

ITIH5

FF

Hyper

109 tumors

MSP

Reduced overall survival

0.008

 

[64]

ITR

NR

Hyper

59 ductal carcinomas, 24 matched normal

IA/CoBRA

Reduced relapse-free survival

0.0041

 

[50]

KLK10

FFPE

Hyper

128 breast carcinomas, 10 breast carcinomas with paired adjacent normal, 10 breast fibroadenomas, and 11 normal

MSP

Reduced disease-free interval Reduced overall survival Increased incidence of relapse

0.0025

0.003

0.026

/

/

3.49

[65]

LHX5

FF

Hyper

125 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.032

2.94

[56]

MLH1

FF

Hyper

86 primary breast cancer tissues (Tunisian cohort)

MSP

Reduced overall survival

0.015

 

[54]

NR2E1

FF

Hyper

241 patients with breast cancer

MethyLight

Reduced time to distant metastasis

0.02

 

[51]

OLIG2

FF

Hyper

115 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.023

2.56

[56]

ONECUT1

FF

Hyper

128 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.023

2.8

[56]

P16

Serum

Hyper

105 tumors, 20 unmatched normal

MSP

Poor prognosis

0.001

5.5

[53]

PITX2

FFPE

Hyper

427 invasive cancers

QM-PCR

Reduced time to distant metastasis

0.004

2.75

[66]

     

Reduced time to distant metastasis

0.013

2.35

 
     

Reduced metastasis-free survival

0.032

2.69

 
 

FF

Hyper

241 patients with breast cancer

MethyLight

High risk of distant recurrence

0.026

 

[51]

     

Reduced time to distant metastasis

<0.001

  
     

Reduced disease-free survival

0.0084

  
     

Reduced overall survival

0.0003

  
 

FF

Hyper

236 node-negative tumors

Array/QM-PCR

Reduced metastasis-free survival

<0.00045

>2.1

[67]

 

FF

Hyper

416 tumors

QM-PCR

Reduced time to distant metastasis

<0.01

1.71

[68]

     

Reduced overall survival

<0.01

1.71

 
     

Reduced metastasis-free survival

<0.01

1.74

 
     

Reduced overall survival

0.02

1.46

 

PITX2/BMP4/c20orf55/fgf5

FF

Hyper

241 patients with breast cancer

MethyLight

Increased risk of distant recurrence Increased risk of distant recurrence

<0.01

<0.01

 

[51]

RARB

FFPE

Hyper

967 primary in situ or invasive breast cancers

MethyLight

Increased breast cancer-specific mortality

NR

1.78

[61]

RASSF1A

FF

Hyper

80 tumors (Tunisian cohort)

MSP

Poor survival

0.014

 

[69]

 

FFPE

Hyper

93 carcinomas, 10 carcinomas with adjacent normal, 10 fibroadenomas, and 11 normal

MSP

Increased incidence of relapse Reduced disease-free survival

0.011

0.028

 

[70]

 

FNA

Hyper

237 patients with suspicious palpable lesions taken prior to surgery

QM-PCR

Reduced disease-free survival

0.031

OR = 2.53

[71]

RECK

NR

Hyper

59 ductal carcinomas, 24 matched normal

IA/CoBRA

Reduced relapse-free survival

0.0001

 

[50]

SFRP1

FF

Hyper

131 tumors, 26 matched normal

MSP

Reduced overall survival

0.045

 

[46]

SFRP2

NR

Hyper

59 ductal carcinomas, 24 matched normal

IA/CoBRA

Reduced relapse-free survival

0.0001

 

[50]

SFRP5

FF

Hyper

14 matched tumors and normal, 155 unmatched tumors

MSP

Reduced overall survival

0.049

4.55

[72]

SYNM

FF/FFPE

Hyper

195 breast cancers

MSP

Reduced recurrence-free survival

0.0282

2.94

[73]

TDGF1

FF

Hyper

109 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.0009

4.08

[56]

TLX3

FF

Hyper

241 patients with breast cancer

MethyLight

Reduced time to distant metastasis

0.008

 

[51]

TUBB3

FF

Hyper

121 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.035

3.19

[56]

TWIST1

FFPE

Hyper

973 primary in situ or invasive breast cancers

MethyLight

Increased breast cancer-specific mortality

NR

1.67

[61]

UAP1L1

NR

Hyper

59 ductal carcinomas, 24 matched normal

IA/CoBRA

Reduced relapse-free survival

0.0005

 

[50]

UGT3A1

NR

Hyper

59 ductal carcinomas, 24 matched normal

IA/CoBRA

Reduced relapse-free survival

0.0018

 

[50]

UNC5A

FF

Hyper

111 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.027

2.74

[56]

ZNF1A1

FF

Hyper

241 patients with breast cancer

MethyLight

Reduced time to distant metastasis

0.044

 

[51]

BTG1

FF

Hypo

124 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.013

2.65

[56]

GSC

FF

Hypo

132 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.002

3.69

[56]

HDAC4

FF

Hypo

117 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.016

2.62

[56]

JUN

FF

Hypo

131 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.025

2.44

[56]

MKI67 (KI-67)

FF

Hypo

116 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.004

3.43

[56]

KIF2C

FF

Hypo

118 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.008

2.65

[56]

KLF4

FF

Hypo

114 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.009

2.63

[56]

KLF5

FF

Hypo

123 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.004

3.56

[56]

LHX2

FF

Hypo

126 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.028

2.32

[56]

MAPK12

FF

Hypo

120 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.001

3.51

[56]

MRD1

FF/serum

Hypo

100 invasive ductal carcinomas with matched normal and blood

MSP

Reduced overall survival

<0.01

 

[74]

ONECUT2

FF

Hypo

127 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.029

2.74

[56]

SPRY1

FF

Hypo

112 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.002

4.0

[56]

TOP1

FF

Hypo

108 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.0005

3.68

[56]

UBE2C

FF

Hypo

119 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.0009

3.57

[56]

VEGF

FF

Hypo

122 tumors, 11 normal (Indian cohort)

MOMA

Increased likelihood of relapse

0.007

3.01

[56]

  1. aHazard ratio given where reported. FF, fresh frozen; FFPE, formalin-fixed paraffin-embedded; FNA, fine-needle aspirate; HR, hazard ratio; Hyper, hypermethylation; Hypo, hypomethylation; IA/CoBRA, infinium array/combined bisulfite restriction enzyme analysis; MOMA, methylation oligonucleotide analysis; MSP, methylation-specific polymerase chain reaction; NR, not reported; OR, odds ratio; Q-BSSeq, quantitative bisulphite sequencing; QM-PCR, quantitative methylation-specific polymerase chain reaction.
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Breast Cancer Research

ISSN: 1465-542X

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