Association between acetaminophen metabolites and CYP2E1 DNA methylation level in neonate cord blood in the Boston Birth Cohort

Li, Yijun; Hong, Xiumei; Liang, Liming; Wang, Xiaobin; Ladd-Acosta, Christine

doi:10.1186/s13148-023-01551-4

Table 3 Results of adjusted models testing for differences in methylation variation

From: Association between acetaminophen metabolites and CYP2E1 DNA methylation level in neonate cord blood in the Boston Birth Cohort

CpG site	Sample variance	Log variance ratio	Difference in Levene’s Residuals	P-value (robust)	FDR	Genomic coordinate (GRCh37/hg19)	Gene Name	Feature category^a	Relation to CpG Island
cg24530264	0.888	− 0.303	− 0.179	2.70E−04*	0.008	chr10:135342620	CYP2E1	Body	South Shore
cg18984983	1.004	− 0.364	− 0.168	9.94E−04*	0.012	chr10:135342936	CYP2E1	Body	South Shore
cg00321709	1.115	− 0.260	− 0.180	1.58E−03*	0.012	chr10:135341933	CYP2E1	Body	Island
cg03134882	0.805	− 0.145	− 0.126	1.68E−03*	0.012	chr10:135341463	CYP2E1	Body	Island
cg19469447	1.296	− 0.142	− 0.140	4.07E−03	0.023	chr10:135341870	CYP2E1	Body	Island
cg13315147	0.818	− 0.119	− 0.097	1.70E−02	0.079	chr10:135341528	CYP2E1	Body	Island
cg05473257	1.327	− 0.116	− 0.108	2.69E−02	0.108	chr10:135341443	CYP2E1	Body	Island
cg25330361	0.516	− 0.214	− 0.095	3.75E−02	0.131	chr10:135342413	CYP2E1	Body	Island
cg23400446	1.423	− 0.090	− 0.090	1.00E−01	0.312	chr10:135342560	CYP2E1	Body	Island
cg21024264	0.139	0.245	0.041	1.42E−01	0.398	chr10:135341025	CYP2E1	1stExon	North Shore
cg26065573	0.081	− 0.241	− 0.028	1.64E−01	0.410	chr10:135339469	CYP2E1	TSS1500	North Shore
cg09208540	0.034	0.162	0.019	1.76E−01	0.410	chr10:135340467	CYP2E1	TSS1500	North Shore
cg07381788	0.063	− 0.121	− 0.021	2.58E−01	0.555	chr10:135340445	CYP2E1	TSS1500	North Shore
cg11445109	1.201	− 0.144	− 0.074	3.12E−01	0.595	chr10:135343248	CYP2E1	Body	South Shore
cg01355198	0.065	− 0.120	− 0.019	3.19E−01	0.595	chr10:135347330	CYP2E1	Body	Open Sea
cg19837601	0.104	0.031	0.022	3.91E−01	0.685	chr10:135340871	CYP2E1;CYP2E1	5'UTR;1stExon	North Shore
cg10862468	0.578	0.016	− 0.035	4.17E−01	0.687	chr10:135342218	CYP2E1	Body	Island
cg05417377	0.074	0.100	0.015	4.42E−01	0.687	chr10:135350807	CYP2E1	Body	Open Sea
cg08472147	0.046	− 0.070	− 0.011	5.04E−01	0.719	chr10:135340583	CYP2E1	TSS1500	North Shore
cg10986462	0.241	0.068	− 0.031	5.14E−01	0.719	chr10:135340539	CYP2E1	TSS1500	North Shore
cg00720244	0.063	− 0.114	− 0.010	5.93E−01	0.790	chr10:135347434	CYP2E1	Body	Open Sea
cg19721068	0.107	− 0.440	− 0.011	6.81E−01	0.867	chr10:135346592	CYP2E1	Body	Open Sea
cg14250048	0.115	− 0.225	0.007	7.84E−01	0.954	chr10:135340785	CYP2E1	TSS200	North Shore
cg00436603	0.104	− 0.019	− 0.003	9.04E−01	0.973	chr10:135340740	CYP2E1	TSS200	North Shore
cg16538390	0.038	0.098	− 0.001	9.35E−01	0.973	chr10:135344917	CYP2E1	Body	South Shelf
cg19571004	0.162	0.076	− 0.002	9.46E−01	0.973	chr10:135340850	CYP2E1	TSS200	North Shore
cg05194426	1.161	0.023	0.002	9.72E−01	0.973	chr10:135343193	CYP2E1	Body	South Shore
cg01465364	0.113	− 0.006	0.001	9.73E−01	0.973	chr10:135340721	CYP2E1	TSS200	North Shore

Results are shown at each of the 28 CpGs located in CYP2E1, between participants with (n = 96) and without (n = 474) acetaminophen detection, sorted by P-value
DNAm DNA methylation, FDR false discovery rate, chr chromosome. The P-values are the original P-values before adjustment for multiple testing. CpG sites with P-value < 1.79 × 10⁻³ (Bonferroni corrected threshold) were marked with asteroid (*). CpG sites with FDR < 0.05 were bolded. Covariates are child sex, delivery type, parity, gestational age, birthweight, maternal age, maternal marital status, prenatal smoking, prenatal alcohol use, intrauterine inflammation, preeclampsia, diabetes mellitus, maternal stress, estimated cell types and 2 surrogate variables. ^aGene feature category of CpG sites obtained from UCSC database: TSS, transcription start site; TSS200, 200 bases from TSS; TSS1500, 1500 bases from TSS; UTR, untranslated region

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ISSN: 1868-7083

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