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

Table 1 Characteristics of Carolina Breast Cancer Study breast cancer cases or tumors evaluated or not evaluated for DNA methylation profile

Characteristic		Cases evaluated for methylation		Cases not evaluated		Pvalue
		(n =517)		(n =163)
		N	(%)	N	(%)
Age	Mean ± SD, years	49.7 ± 11.9		52.2 ± 11.9
	<50 years	318	(62)	84	(52)	0.02
	50+ years	199	(38)	78	(48)
Race
	White/Other^a	301	(58)	106	(65)	0.12
	African-American	216	(42)	57	(35)
Menopausal status
	Premenopausal	275	(53)	76	(47)	0.14
	Postmenopausal	242	(47)	87	(53)
Stage^b
	I	178	(37)	68	(45)	0.37
	II	245	(51)	67	(44)
	III	45	(9)	12	(8)
	IV	13	(3)	4	(3)
Primary tumor size
	≤2 cm	250	(50)	87	(57)	0.28
	>2-5 cm	205	(41)	52	(34)
	>5 cm	42	(9)	13	(9)
Lymph node status
	Negative	291	(58)	101	(66)	0.11
	Positive	207	(42)	53	(34)
Hormone receptor expression
	ER⁺/PR⁺	250	(50)	62	(42)	0.38
	ER⁺/PR^-	48	(10)	17	(12)
	ER^-/PR⁺	39	(8)	15	(10)
	ER^-/PR^-	163	(33)	53	(36)
Combined tumor grade^c
	I	126	(25)	47	(29)	0.48
	II	156	(30)	49	(30)
	II	228	(45)	65	(40)
Histologic type
	Ductal^d	388	(75)	122	(75)	0.23
	Ductal variants^e	13	(3)	9	(5)
	Poorly differentiated^f	22	(4)	3	(2)
	Lobular^g	46	(9)	13	(8)
	Mixed lobular/Ductal	48	(9)	16	(10)
IHC intrinsic subtype^h
	Luminal A	212	(51)	42	(51)	0.76
	Luminal B	65	(16)	12	(15)
	Basal-like	86	(21)	14	(17)
	HER2⁺/HR^-	26	(6)	7	(8)
	Unclassified	24	(6)	7	(8)
p53 mutation status
	Positive	218	(42)	47	(34)	0.08
	Negative	297	(58)	91	(66)

^aThe white/other cases evaluated included 291 Caucasians, 3 American Indians, 6 Asians, and 1 other. ^bAccording to the American Joint Committee on Cancer breast tumor staging guidelines. ^cNottingham grade based on mitotic index, histologic grade, and nuclear grade. ^dDuctal not otherwise specified (n = 372), medullary (n = 3), neuroendocrine (n =2), apocrine (n = 2), and other mixed (n = 9). ^eDuctal variants include mucinous (n =8), papillary (n = 1), and cribriform (n = 4). ^fPoorly differentiated include metaplastic carcinoma (n = 6), anaplastic carcinoma (n =3), and undifferentiated high grade carcinoma (n = 13). ^gLobular, classic, and/or variant (n = 46). ^hIntrinsic subtype was determined by estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status determined by medical records or immunohistochemistry (IHC), and IHC staining for CK5, CK6, and epidermal growth factor receptor. HR, hormone receptor; SD, standard deviation.