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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.