Skip to main content

Table 2 Characteristics of the four methylation-based consensus clusters

From: DNA methylation profiling in the Carolina Breast Cancer Study defines cancer subclasses differing in clinicopathologic characteristics and survival

Characteristic

Cluster 1

Cluster 2

Cluster 3

Cluster 4

Pvalue

(n =123)

(n =108)

(n =99)

(n =187)

N

(%)

N

(%)

N

(%)

N

(%)

Age, years

         

<50

73

(59)

82

(76)

54

(55)

109

(58)

0.006

50+

50

(41)

26

(24)

45

(45)

78

(42)

 

Race

         

White/Other

66

(54)

53

(49)

58

(59)

124

(66)

0.02

African-American

57

(46)

55

(51)

41

(41)

63

(34)

 

Menopausal status

         

Postmenopausal

61

(50)

39

(36)

51

(52)

91

(49)

0.09

Premenopausal

62

(50)

69

(64)

48

(48)

96

(51)

 

Stage

         

I

58

(49)

26

(27)

24

(25)

70

(41)

0.02

II

48

(40)

58

(60)

56

(60)

83

(48)

 

III

12

(10)

9

(9)

11

(12)

13

(8)

 

IV

1

(1)

4

(4)

3

(3)

5

(3)

 

Missing

4

 

11

 

5

 

16

  

Primary tumor size

         

≤2 cm

72

(60)

35

(35)

36

(38)

107

(59)

0.0003

>2-5 cm

39

(33)

53

(54)

49

(51)

64

(35)

 

>5 cm

9

(7)

11

(11)

11

(11)

11

(6)

 

Missing

3

 

9

 

3

 

5

  

Lymph node status

         

Positive

44

(37)

40

(39)

48

(50)

75

(42)

0.24

Negative

76

(63)

62

(61)

48

(50)

105

(58)

 

Missing

3

 

6

 

3

 

7

  

Tumor grade

         

I

29

(24)

3

(3)

17

(17)

77

(42)

<0.0001

II

34

(28)

16

(15)

40

(40)

66

(36)

 

III

58

(48)

87

(82)

42

(43)

41

(22)

 

Missing

2

 

2

   

3

  

Estrogen receptor status

         

Positive

56

(47)

11

(11)

79

(81)

153

(83)

<0.0001

Negative

64

(53)

90

(89)

18

(19)

31

(17)

 

Missing

3

 

7

 

2

 

3

  

Hormone receptor status

         

Positive

69

(58)

20

(20)

83

(86)

166

(90)

<0.0001

Negative

51

(42)

81

(80)

13

(14)

18

(10)

 

Missing

3

 

7

 

3

 

3

  

Histologic type

         

Ductal NOS

98

(80)

89

(82)

78

(79)

123

(66)

<0.0001

Ductal variants

3

(2)

0

(0)

4

(4)

6

(3)

 

Poorly differentiated

7

(6)

11

(10)

2

(2)

2

(1)

 

Lobular

8

(6)

1

(1)

7

(7)

30

(16)

 

Mixed lobular

7

(6)

7

(7)

8

(8)

26

(14)

 

Intrinsic subtype (IHC)

         

Luminal A

48

(49)

12

(14)

52

(64)

100

(69)

<0.0001

Luminal B

12

(12)

5

(6)

17

(21)

31

(22)

 

Basal-like

25

(25)

54

(61)

3

(4)

4

(3)

 

HER2+/ER-

6

(6)

7

(8)

8

(10)

5

(3)

 

Unclassified

8

(8)

10

(11)

1

(1)

5

(3)

 

Missing

24

 

20

 

18

 

42

  

p53 mutation status

         

Mutant

59

(48)

90

(83)

25

(25)

44

(24)

<0.0001

Wild-type

64

(52)

18

(17)

74

(75)

141

(76)

 

Missing

      

2

  

EGFR status

         

Positive

34

(32)

75

(75)

9

(10)

11

(7)

<0.0001

Negative

71

(68)

25

(25)

78

(90)

149

(93)

 

Missing

18

 

8

 

12

 

27

  

HER2 status

         

Positive

25

(20)

16

(15)

31

(31)

50

(27)

0.02

Negative

97

(80)

92

(85)

68

(69)

135

(73)

 

Missing

1

     

2

  
  1. Hormone receptor (HR) status: positive: estrogen receptor-positive (ER+) or progesterone receptor-positive (PR+) or both; negative: ER- and PR-. Consensus methylation clusters 1 to 4 based on the most variant 167 CpG (cytosine preceding a guanosine) sites. Intrinsic subtypes: luminal A (ER+ and/or PR+, HER2-), luminal B (ER+ and/or PR+, HER2+), basal-like (ER-, PR-, HER2-, CK5+ and/or CK6+ or EGFR+), HER2+/HR- (ER-/PR-/HER2+), and unclassified (all markers negative). EGFR, epidermal growth factor receptor; HER2, human epidermal growth factor receptor 2; IHC, immunohistochemistry; NOS, not otherwise specified.
Back to article page

Breast Cancer Research

ISSN: 1465-542X

Contact us