Methylation of leukocyte DNA and ovarian cancer: relationships with disease status and outcome

Fridley, Brooke L; Armasu, Sebastian M; Cicek, Mine S; Larson, Melissa C; Wang, Chen; Winham, Stacey J; Kalli, Kimberly R; Koestler, Devin C; Rider, David N; Shridhar, Viji; Olson, Janet E; Cunningham, Julie M; Goode, Ellen L

doi:10.1186/1755-8794-7-21

BMC Medical Genomics

Table 2 CpG sites associated with disease status (p ≤ 5×10 ^-7 )

From: Methylation of leukocyte DNA and ovarian cancer: relationships with disease status and outcome

Probe ID	Ch	Position (bp)	Nearest genes	Location of nearest gene (bp)^#	Location to Island^{^}	Meta-Analysis^§		Batch 1		Batch 2		Batch 3
						$\hat{β}$	P	$\hat{β}$	P	$\hat{β}$	P	$\hat{β}$	P
cg04834572*	10	76868766	DUSP13	76854190-76868970	Shelf	-0.65	1.6E-14	-0.82	2.1E-4	-0.55	6.0E-6	-0.73	1.1E-6
cg11722531	19	1449857	APC2	1450148-1473243	Shore	-0.62	2.7E-13	-0.64	3.5E-3	-0.54	6.4E-6	-0.74	1.3E-6
cg10414058*	5	141017903	RELL2	141016517-	Shore	-0.94	6.3E-12	-1.13	3.5E-8	-0.71	7.1E-10	-1.05	9.0E-14
			HDAC3	141020631
			HDAC3	141000443-141016423
cg14580567	4	145567271	HHIP	145567148-145659881	Island	-0.56	5.6E-11	-0.49	0.024	-0.55	3.8E-6	-0.61	9.3E-5
cg08245789	22	40289538	ENTHD1	40139049-40289794		-0.56	3.6E-10	-0.66	4.0E-3	-0.43	3.9E-4	-0.69	6.5E-6
cg27623214	19	58485726	C19orf18 ^†	58469805-58485902		-0.52	1.3E-9	-0.66	2.9E-3	-0.52	1.4E-5	-0.45	3.4E-3
cg23877385	15	59908652	GCNT3	59903982-59912210		-0.52	2.2E-9	-0.46	0.043	-0.53	1.3E-5	-0.52	6.3E-4
cg26150490	X	47863595	SPACA5	47863734-47869130	Island	-0.50	3.6E-9	-0.34	0.10	-0.54	6.8E-6	-0.52	6.6E-4
cg26150490	X	47863595	ZNF182	47834250-47863394	Island	-0.50	3.6E-9	-0.34	0.10	-0.54	6.8E-6	-0.52	6.6E-4
cg22336401	9	140336227	ENTPD8	140328816-140335901	Island	-0.50	5.3E-9	-0.27	0.24	-0.51	2.5E-5	-0.60	9.1E-5
cg20775254	2	95940705	PROM2	95940201-95957056		-0.53	6.1E-9	-0.58	5.3E-3	-0.41	8.2E-4	-0.69	5.6E-6
cg19280776*	8	82024586	PAG1	81880045-82024303	Shore	0.49	1.0E-8	0.60	6.2E-3	0.52	1.4E-5	0.38	0.013
cg07634191	8	27850178	SCARA5	27727399-27850369		-0.48	1.8E-8	-0.50	0.025	-0.39	1.2E-3	-0.61	4.5E-5
cg21244955	22	21192955	PI4KA	21061979-21213100		-0.49	2.2E-8	-0.47	0.039	-0.48	6.6E-5	-0.50	1.3E-3
cg18159180	6	43022213	CUL7	43005355-43021683	Shore	-0.48	2.2E-8	-0.35	0.12	-0.57	2.8E-6	-0.41	8.0E-3
cg18159180	6	43022213	MRPL2	43021767-43027242	Shore	-0.48	2.2E-8	-0.35	0.12	-0.57	2.8E-6	-0.41	8.0E-3
cg04439215	13	45768901	KCTD4	45766988-45775175		-0.49	2.4E-8	-0.65	4.4E-3	-0.37	2.2E-3	-0.60	1.0E-4
cg04439215	13	45768901	GTF2F2	45694631-45858240		-0.49	2.4E-8	-0.65	4.4E-3	-0.37	2.2E-3	-0.60	1.0E-4
cg26787239	5	132008525	IL4	132009678-132018370		-0.48	2.9E-8	-0.50	0.025	-0.50	3.4E-5	-0.43	4.8E-3
cg07259382	4	164536228	MARCH1 ^†	164445450-165304407		-0.48	3.0E-8	-0.58	8.5E-3	-0.43	3.1E-4	-0.50	1.2E-3
cg14808739	17	17741098	SREBF1	17714663-17740325	Shore	-0.48	3.7E-8	-0.41	0.063	-0.52	2.3E-5	-0.44	3.8E-3
cg00065385	9	111623395	ACTL7A	111624603-111626035		-0.47	6.1E-8	-0.50	0.026	-0.49	5.0E-5	-0.43	6.9E-3
cg04721883	X	103499577	ESX1	103494719-103499599	Island	-0.46	7.6E-8	-0.40	0.068	-0.38	1.7E-3	-0.62	4.6E-5
cg21400640	X	12992967	TMSB4X	12993226-12995346	Shore	-0.46	1.1E-7	-0.50	0.029	-0.46	1.4E-4	-0.44	4.0E-3
cg11871280	12	60082038	SLC16A7	59989821-60183636		-0.45	1.7E-7	-0.24	0.28	-0.51	2.4E-5	-0.46	3.1E-3
cg09261015	X	103499647	ESX1	103494719-103499599	Island	-0.45	2.1E-7	-0.46	0.046	-0.39	1.1E-3	-0.54	4.7E-4
cg18731813	X	100805683	ARMCX1	100805514-100809683	Shelf	-0.44	2.4E-7	-0.23	0.30	-0.46	1.3E-4	-0.51	7.3E-4
cg23279136	X	74375966	ABCB7	74273105-74376132		-0.44	3.2E-7	-0.62	6.3E-3	-0.33	5.7E-3	-0.54	4.9E-4
cg02254461	3	39195904	CSRNP1	39183342-39195102	Shore	-0.44	3.6E-7	-0.37	0.10	-0.48	9.1E-5	-0.42	6.1E-3
cg26246138	X	18372612	SCML2	18257433-18372844	Island	-0.44	3.8E-7	-0.37	0.096	-0.37	2.3E-3	-0.57	1.6E-4
cg24959428*	1	89829951	GBP6	89829436-89853719		-0.44	4.1E-7	-0.50	0.025	-0.42	5.2E-4	-0.44	4.4E-3
cg05498681	20	35973318	SRC	35973088-36033821	Shore	-0.44	4.8E-7	-0.17	0.45	-0.53	1.3E-5	-0.41	8.1E-3
cg01377911	19	49568036	NTF4	49564397-49567124		-0.43	5.0E-7	-0.38	0.086	-0.37	2.3E-3	-0.55	2.5E-4

^#Locations based on NCBI (http://www.ncbi.nlm.nih.gov), build 37.
^Shore CpG sites defined to be within +/- 2 kb from CpG island; Shelf CpG sites defined to be within +/- 2kb of CpG Shore.
^§All tests for heterogeneity of effects across the three batches were non-significant (p > 0.05); analysis adjusted for age at first live birth, alcohol use, smoking status, enrollment year, and recruitment state; a negative parameter estimate indicates lower methylation in the cases as compared to the control (e.g., cases where hypomethylated).
*Same CpG site found to be associated with EOC risk (p ≤ 0.001) in a prior report [14].
^†CpG sites near this gene found to be associated with EOC risk in a prior report [14].

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ISSN: 1755-8794

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