Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions

Li, Qingqin S.; Sun, Yu; Wang, Tania

doi:10.1186/s13148-020-00944-z

Table 2 Replicated DMPs associated with Braak stage

From: Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions

Name	Chr	Pos	Gene annotation	Strand	Relation to Island	UCSC RefGene Group	This study				Smith et al. meta-analysis
							STG		IFG		ES	p value	Brain region
							beta	p value	beta	p value	ES	p value	Brain region
cg15645660	1	55,247,356		+	Island	Body	0.09	1.03E−03	0.09	2.28E−05	0.04	2.12E−08	Prefrontal Cortex
cg15645660	1	55,247,356		+	Island	Body	0.09	1.03E−03	0.09	2.28E−05	0.03	4.67E−10	Cross Cortex
cg17104258	1	1.67E+08		−	Island	Body	− 0.12	8.72E−03	− 0.22	5.99E−06	− 0.02	6.27E−11	Cross Cortex
cg17104258	1	1.67E+08		−	Island	Body	− 0.12	8.72E−03	− 0.22	5.99E−06	− 0.03	2.60E−08	TG
cg12307200	3	1.89E+08	TPRG1;TPRG1-AS1	+	N Shore		− 0.05	7.18E−04	− 0.04	8.65E−05	− 0.02	2.19E−11	Prefrontal Cortex
cg12307200	3	1.89E+08	TPRG1;TPRG1-AS1	+	N Shore		− 0.05	7.18E−04	− 0.04	8.65E−05	− 0.02	2.72E−12	TG
cg12307200	3	1.89E+08	TPRG1;TPRG1-AS1	+	N Shore		− 0.05	7.18E−04	− 0.04	8.65E−05	− 0.02	4.48E−16	Cross Cortex
cg11964461	5	1.8E+08	RASGEF1C	−	OpenSea	5′UTR	0.01	1.58E−01	0.03	1.01E−04	0.01	9.48E−08	Cross Cortex
cg00921266	7	27,153,663	HOXA3;HOXA-AS2;HOXA3	−	N Shore	5′UTR;TSS200	0.11	8.39E−05	0.04	2.01E−01	0.03	8.94E−10	Prefrontal Cortex
cg00921266	7	27,153,663	HOXA3;HOXA-AS2;HOXA3	−	N Shore	5′UTR;TSS200	0.11	8.39E−05	0.04	2.01E−01	0.02	9.25E−09	Cross Cortex
cg05066959	8	41,519,308	ANK1	−	OpenSea	TSS1500;Body	0.10	2.91E−02	0.10	2.04E−05	0.02	1.45E−12	Cross Cortex
cg05066959	8	41,519,308	ANK1	−	OpenSea	TSS1500;Body	0.10	2.91E−02	0.10	2.04E−05	0.04	4.58E−13	TG
cg05066959	8	41,519,308	ANK1	−	OpenSea	TSS1500;Body	0.10	2.91E−02	0.10	2.04E−05	0.03	7.35E−10	Prefrontal Cortex
cg05066959	8	41,519,308	ANK1	−	OpenSea	TSS1500;Body	0.10	2.91E−02	0.10	2.04E−05	0.06	2.93E−09	EC
cg23968456	10	73,521,631		−	OpenSea	Body	0.11	1.95E−02	0.09	2.37E−05	0.01	1.09E−09	Cross Cortex
cg23968456	10	73,521,631		−	OpenSea	Body	0.11	1.95E−02	0.09	2.37E−05	0.01	1.06E−09	TG
cg10469774	11	44,642,932		−	OpenSea		0.05	2.23E−03	0.07	4.77E−05	0.01	7.26E−09	Cross Cortex
cg07883124	13	1.14E+08	MCF2L	−	Island	Body;1stExon	0.03	3.52E−02	0.05	8.57E−06	0.02	9.10E−13	Cross Cortex
cg07883124	13	1.14E+08	MCF2L	−	Island	Body;1stExon	0.03	3.52E−02	0.05	8.57E−06	0.02	6.40E−08	Prefrontal Cortex
cg09448088	13	1.14E+08		−	Island	Body	0.02	8.69E−02	0.06	3.95E−09	0.01	1.04E−08	Cross Cortex
cg26127778	15	93,617,141	RGMA	−	Island	1stExon;TSS1500;Body;5′UTR	− 0.05	3.52E−05	− 0.03	1.88E−03	− 0.02	4.88E−08	TG
cg17400113	15	93,617,146	RGMA	−	Island	1stExon;TSS1500;Body;5′UTR	− 0.03	1.23E−03	− 0.03	1.75E−05	− 0.01	1.15E−08	Cross Cortex
cg17400113	15	93,617,146	RGMA	−	Island	1stExon;TSS1500;Body;5′UTR	− 0.03	1.23E−03	− 0.03	1.75E−05	− 0.02	3.75E−08	TG
cg09109520	16	57,673,258	GPR56	−	OpenSea	5′UTR;1stExon	0.06	9.14E−05	0.03	1.39E−01	0.02	9.00E−11	Cross Cortex
cg09109520	16	57,673,258	GPR56	−	OpenSea	5′UTR;1stExon	0.06	9.14E−05	0.03	1.39E−01	0.02	2.53E−10	Prefrontal Cortex
cg03169557	16	89,598,950	SPG7	+	OpenSea	Body	0.13	4.99E−02	0.21	1.33E−06	0.01	3.15E−08	Prefrontal Cortex
cg03169557	16	89,598,950	SPG7	+	OpenSea	Body	0.13	4.99E−02	0.21	1.33E−06	0.02	2.71E−10	TG
cg03169557	16	89,598,950	SPG7	+	OpenSea	Body	0.13	4.99E−02	0.21	1.33E−06	0.01	5.41E−11	Cross Cortex
cg03169557	16	89,598,950	SPG7	+	OpenSea	Body	0.13	4.99E−02	0.21	1.33E−06	0.02	4.41E−09	EC
cg19803550	17	1,637,391	RP11-961A15.1	+	Island	Body	0.14	1.91E−02	0.13	1.67E−05	0.01	1.06E−08	Cross Cortex
cg19803550	17	1,637,391	RP11-961A15.1	+	Island	Body	0.14	1.91E−02	0.13	1.67E−05	0.01	3.68E−08	Prefrontal Cortex
cg05810363	17	74,475,270		−	Island	Body	0.12	6.05E−02	0.16	6.73E−07	0.03	2.25E−11	TG
cg05810363	17	74,475,270		−	Island	Body	0.12	6.05E−02	0.16	6.73E−07	0.02	2.01E−10	Cross Cortex
cg13076843	17	74,475,294		+	Island	Body	0.07	3.13E−02	0.10	1.02E−04	0.03	7.31E−10	Prefrontal Cortex
cg13076843	17	74,475,294		+	Island	Body	0.07	3.13E−02	0.10	1.02E−04	0.02	7.57E−13	Cross Cortex
cg13076843	17	74,475,294		+	Island	Body	0.07	3.13E−02	0.10	1.02E−04	0.03	2.97E−11	TG
cg12163800	17	74,475,355	RHBDF2	+	Island	Body	0.08	1.92E−03	0.10	9.19E−06	0.01	5.13E−09	Cross Cortex
cg12163800	17	74,475,355	RHBDF2	+	Island	Body	0.08	1.92E−03	0.10	9.19E−06	0.02	2.06E−08	Prefrontal Cortex
cg12163800	17	74,475,355	RHBDF2	+	Island	Body	0.08	1.92E−03	0.10	9.19E−06	0.02	5.85E−09	TG
cg12309456	17	74,475,402		−	Island	Body	0.09	2.46E−02	0.10	7.68E−06	0.02	1.33E−08	TG
cg12309456	17	74,475,402		−	Island	Body	0.09	2.46E−02	0.10	7.68E−06	0.01	4.09E−08	Cross Cortex
cg08481112	19	2,544,100	GNG7	+	S Shore	5′UTR	0.07	4.81E−05	0.03	7.27E−02	0.02	2.84E−08	Prefrontal Cortex
cg23449541	21	47,855,893	PCNT	−	Island	Body	0.04	3.16E−02	0.07	8.45E−06	0.01	7.49E−08	Cross Cortex
cg23449541	21	47,855,893	PCNT	−	Island	Body	0.04	3.16E−02	0.07	8.45E−06	0.02	9.43E−11	TG
cg00621289	21	47,855,916	PCNT	−	Island	Body	0.04	1.43E−02	0.06	2.51E−05	0.01	4.69E−11	Cross Cortex

Chr: chromosome; Pos: base pair position in reference to human genome hg19; Gene Annotation: gene annotation in reference to Gencode Basic V12; beta coefficient and p value was reported from the limma robust regression model for this study for each DMP, while the effect size (ES) and corresponding unadjusted p value from the inverse variance fixed effects meta-analysis model was shown for the Smith et al. meta-analysis. In addition, ES from the Smith et al. meta-analysis has been multiplied by six to demonstrate the difference between Braak stage 0 and Braak stage VI samples. This was not done for this study

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ISSN: 1868-7083

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