Epigenome-wide association study for lifetime estrogen exposure identifies an epigenetic signature associated with breast cancer risk

Johansson, Annelie; Palli, Domenico; Masala, Giovanna; Grioni, Sara; Agnoli, Claudia; Tumino, Rosario; Giurdanella, Maria Concetta; Fasanelli, Francesca; Sacerdote, Carlotta; Panico, Salvatore; Mattiello, Amalia; Polidoro, Silvia; Jones, Michael E.; Schoemaker, Minouk J.; Orr, Nick; Tomczyk, Katarzyna; Johnson, Nichola; Fletcher, Olivia; Perduca, Vittorio; Baglietto, Laura; Dugué, Pierre-Antoine; Southey, Melissa C.; Giles, Graham G.; English, Dallas R.; Milne, Roger L.; Severi, Gianluca; Ambatipudi, Srikant; Cuenin, Cyrille; Chajès, Veronique; Romieu, Isabelle; Herceg, Zdenko; Swerdlow, Anthony J.; Vineis, Paolo; Flanagan, James M.

doi:10.1186/s13148-019-0664-7

Table 1 List of the 42 target CpG sites included in the targeted bisulfite sequencing

From: Epigenome-wide association study for lifetime estrogen exposure identifies an epigenetic signature associated with breast cancer risk

HM450K probe	Chr	Position	Nearest gene	Distance to gene	EWAS of ELEE in EPIC-Italy^b
HM450K probe	Chr	Position	Nearest gene	Distance to gene	Estimate	SE	P value	Q value
cg01893629	chr12	34494825	ALG10	313588	− 0.14	0.03	8.15E−05	4.96E−02
cg08254089^a	chr20	36933189	BPI	0	− 0.28	0.08	7.04E−05	4.78E−02
cg21590238	chr12	121454837	C12orf43	536	− 0.29	0.08	2.67E−06	1.44E−02
cg21153102	chr15	41252147	CHAC1	3429	− 0.43	0.14	6.16E−05	4.58E−02
cg03340215^a	chr15	83315615	CPEB1	0	− 0.31	0.08	4.78E−05	4.21E−02
cg06968859	chr2	80724209	CTNNA2	0	− 0.26	0.05	2.52E−09	1.02E−03
cg12105860^a	chr12	31742801	DENND5B	0	0.14	0.03	1.58E−06	1.21E−02
cg16840364^a	chr4	84539569	GPAT3	12541	− 0.14	0.06	4.77E−05	4.21E−02
cg08835688	chr7	50849931	GRB10	0	− 0.14	0.03	4.50E−05	4.11E−02
cg08349826	chr16	10346403	GRIN2A	69791	− 0.11	0.04	4.19E−05	4.02E−02
cg23681866	chr6	29895175	HLA-J	0	− 1.33	0.31	2.17E−05	3.13E−02
cg22968966	chr16	22959875	HS3ST2	32215	− 0.40	0.12	7.95E−05	4.92E−02
cg15127563	chr2	231729487	ITM2C	132	0.36	0.09	1.77E−05	2.95E−02
cg20020161	chr2	231732669	ITM2C	0	− 0.14	0.04	4.49E−05	4.11E−02
cg22097768	chr17	61615913	KCNH6	0	− 0.20	0.05	4.88E−05	4.25E−02
cg17969123	chr19	18745971	KLHL26	1865	− 0.15	0.04	3.18E−05	3.65E−02
cg05422360	chrX	75648455	MAGEE1	0	− 0.44	0.12	1.72E−07	5.26E−03
cg01768446	chr16	89982419	MC1R	1866	− 0.13	0.03	4.57E−05	4.13E−02
cg25372296	chr1	98510328	MIR137HG	0	0.33	0.09	3.83E−06	1.65E−02
cg04519403^a	chr5	79298951	MTX3	11862	− 0.24	0.05	7.51E−06	2.20E−02
cg12091786	chr20	61877942	NKAIN4	0	− 0.37	0.10	2.07E−05	3.06E−02
cg25279613^a	chr7	24956523	OSBPL3	0	0.20	0.06	4.95E−06	1.96E−02
cg24536703	chr11	77183438	PAK1	0	− 0.32	0.09	2.71E−05	3.43E−02
cg24036523	chr14	73712256	PAPLN	0	− 0.45	0.11	3.05E−05	3.65E−02
cg16720405	chr3	122790178	PDIA5	0	− 0.17	0.05	5.17E−05	4.33E−02
cg13674411	chr1	204232677	PLEKHA6	0	0.11	0.03	3.50E−05	3.76E−02
cg20684174	chr11	7541255	PPFIBP2	0	− 0.13	0.03	1.23E−05	2.67E−02
cg01430588^a	chr17	56769767	RAD51C	194	− 0.32	0.09	6.04E−05	4.51E−02
cg22273487	chr20	32580931	RALY	525	0.19	0.05	1.60E−05	2.84E−02
cg22343083	chr8	54786401	RGS20	0	− 0.30	0.07	1.92E−06	1.26E−02
cg22758104	chr17	50465	RPH3AL	11713	− 0.23	0.06	4.62E−07	6.07E−03
cg16733643^a	chr1	41575522	SCMH1	0	− 0.42	0.11	5.00E−05	4.25E−02
cg17588491	chr22	25198892	SGSM1	3242	− 0.17	0.04	4.41E−05	4.06E−02
cg13971030	chr11	35366721	SLC1A2	0	− 0.49	0.14	9.19E−06	2.41E−02
cg17567562^a	chr3	47687980	SMARCC1	0	− 0.48	0.11	1.18E−05	2.66E−02
cg10298859	chr13	112883993	SPACA7	146656	− 0.20	0.04	2.26E−07	5.26E−03
cg19216791	chr19	5568216	TINCR	210	− 0.25	0.07	4.13E−05	4.02E−02
cg25936380	chr2	120981591	TMEM185B	606	− 0.29	0.07	2.22E−07	5.26E−03
cg01824466^a	chr8	95959531	TP53INP1	0	− 0.23	0.08	8.08E−05	4.96E−02
cg26657235	chr6	150378972	ULBP3	4367	− 0.12	0.03	1.32E−05	2.76E−02
cg08551047	chr15	91473569	UNC45A	0	− 0.58	0.14	2.87E−06	1.46E−02
cg20394620^a	chrX	48541924	WAS	260	− 0.20	0.05	3.02E−06	1.46E−02

SE standard error
^aMarked probes did not pass quality control in the targeted sequencing data and were not included in the analysis of the methylation index
^bResult from the EWAS of ELEE in EPIC-Italy (n = 216, dataset 2). The estimates correspond to regression coefficients from a mixed-effects linear regression model (percentage change in DNA methylation per unit longer ELEE), and P values from the beta regression model, which have been corrected for multiple testing using FDR (Q values)

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ISSN: 1868-7083

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