DNA methylation sites in early adulthood characterised by pubertal timing and development: a twin study

Sehovic, Emir; Zellers, Stephanie M.; Youssef, Markus K.; Heikkinen, Aino; Kaprio, Jaakko; Ollikainen, Miina

doi:10.1186/s13148-023-01594-7

Clinical Epigenetics

Table 2 CpG sites significantly associated (p < 1 × 10^–5) with pubertal development scale (PDS) and pubertal age (PA)

From: DNA methylation sites in early adulthood characterised by pubertal timing and development: a twin study

Original model and CpG ID	Individual platform effect size (450 K; EPIC)	Standardised effect size*	P value	Q p value‡	Chr	Gene	Mean (M)†	Mean (F)†	Wilcoxon two-sample test (p)§
PDS-12
cg15030014	− 0.025; − 0.037	− 0.175	2.85E−07	1.000	7	C7orf20	0.886	0.890	1.000
cg25614726	− 0.023; − 0.013	− 0.169	7.61E−07	1.000	1	APITD1	0.378	0.399	2.31E−12
cg08273672	− 0.01; − 0.01	− 0.161	2.59E−06	1.000	4	UCHL1	0.754	0.760	0.131
cg05038881	− 0.026; − 0.004	− 0.161	2.65E−06	1.000	1	APITD1	0.430	0.451	3.32E−09
cg26027669	0.014; 0.012	0.159	3.38E−06	1.000	1	GFI1	0.054	0.048	9.03E−14
cg22064581	0.004; − 0.001	0.156	5.30E−06	1.000	6		0.032	0.031	1.000
cg08091771	− 0.012; − 0.011	− 0.156	5.57E−06	1.000	3	PTPRG	0.705	0.708	1.000
cg26489369	− 0.009; − 0.002	− 0.155	6.19E−06	1.000	6	HLA-DQA2	0.950	0.952	0.228
cg06993494	− 0.009; − 0.017	− 0.153	8.26E−06	1.000	11	OR5A1	0.966	0.967	0.132
PDS-12—Males
cg25801636	0.009; 0.037	0.245	8.46E−07	0.007	2		0.949	0.949	1.000
cg13653963	0.003; 0.018	0.242	9.10E−07	0.001	9	C9orf98	0.965	0.967	1.11E−04
cg14609721	0.015; − 0.005	0.249	1.04E−06	0.750	1	DEPDC1	0.019	0.018	0.098
cg03468249	0.008; 0	0.250	1.16E−06	0.932	2		0.026	0.025	1.000
cg09736922	− 0.029; − 0.006	− 0.245	1.99E−06	0.960	3	THPO	0.753	0.757	1.000
cg22539434	− 0.015; − 0.006	− 0.246	2.03E−06	1.000	7	GLI3	0.963	0.962	0.937
cg15680660	− 0.012; − 0.012	− 0.246	2.05E−06	1.000	3	XYLB	0.949	0.947	1.000
cg04547799	− 0.003; − 0.007	− 0.234	5.80E−06	0.860	6	HMGN3	0.029	0.030	0.001
cg05797363	0.008; − 0.002	0.232	6.16E−06	0.700	1	DEPDC1	0.016	0.016	1.000
cg04052235	0.03; 0.062	0.231	7.46E−06	0.722	11		0.422	0.433	1.49E−05
cg06002616	0.021; 0.105	0.225	8.37E−06	0.039	8	SPAG1	0.074	0.071	1.000
cg04769618	0.011; 0.015	0.230	8.70E−06	0.874	10	LOC387647	0.033	0.034	1.000
cg14685946	− 0.005; − 0.034	− 0.222	8.73E−06	0.002	2	ACSL3	0.924	0.925	1.000
PDS-12 – Females
cg07581365	− 0.005; 0	− 0.233	1.54E−07	1.000	17	CBX8	0.031	0.031	1.000
cg06988547	− 0.036; 0.003	− 0.231	1.87E−07	1.000	1		0.909	0.910	1.000
cg18397726	− 0.04; − 0.024	− 0.217	1.38E−06	1.000	14	CHGA	0.949	0.949	0.016
cg07844563	− 0.002; − 0.014	− 0.206	2.25E−06	0.001	1	LOC653566	0.959	0.956	0.038
cg08883485	− 0.033; − 0.085	− 0.209	2.80E−06	0.660	1	NAV1	0.452	0.473	4.36E−05
cg23204278	0.001; 0.001	0.211	2.87E−06	1.000	18		0.012	0.012	1.000
cg10669219	− 0.02; − 0.008	− 0.207	4.34E−06	1.000	5		0.822	0.827	0.863
cg19237923	− 0.015; − 0.035	− 0.204	5.39E−06	0.710	1	NTRK1	0.671	0.699	7.53E−39
cg09550127	− 0.008; − 0.01	− 0.203	6.90E−06	1.000	6		0.929	0.936	1.24E−04
cg17052466	− 0.006; 0.001	− 0.201	8.25E−06	1.000	11	TSSC4	0.952	0.956	1.41E−06
PDS-14—Males
cg04239863	0; − 0.056	− 0.273	8.15E−09	9.38E−09	16		0.831	0.841	0.004
cg03115019	− 0.028; − 0.148	− 0.256	5.28E−07	0.040	17	FN3K	0.837	0.848	0.012
cg22325292	− 0.044; − 0.291	− 0.252	7.82E−07	0.038	17	FN3K	0.719	0.729	1.000
cg15142913	− 0.016; − 0.001	− 0.259	7.88E−07	0.952	8	PTP4A3	0.929	0.931	1.000
cg00008671	− 0.01; − 0.038	− 0.247	2.06E−06	0.350	10	FAM190B	0.238	0.228	2.57E−04
cg14466923	0.002; 0.011	0.232	3.40E−06	1.73E−04	6	COL11A2	0.943	0.943	1.000
cg21759953	0.006; 0.006	0.242	5.09E−06	1.000	2	GLI2	0.917	0.918	1.000
cg18223453	0.005; 0.054	0.227	6.73E−06	0.001	17	TBX4	0.682	0.735	3.59E−82
cg02763540	− 0.016; 0.002	− 0.235	8.71E−06	0.922	19	UHRF1	0.804	0.812	0.049
cg19238380	− 0.018; − 0.031	− 0.235	9.49E−06	0.969	1	LMNA	0.473	0.487	1.63E−09
cg24786174	− 0.067; − 0.074	− 0.236	9.83E−06	1.000	18	ZNF516	0.542	0.528	1.000
cg04230403	− 0.001; − 0.017	− 0.224	9.98E−06	0.001	10	FAS	0.026	0.026	1.000
PDS-14—Females
cg20599748	− 0.005; − 0.012	− 0.238	7.39E−08	0.390	14	SERPINA10	0.953	0.955	1.000
cg13634653	− 0.002; − 0.006	− 0.212	1.70E−06	0.047	15		0.969	0.970	0.002
cg17965926	0.001; 0.009	0.203	2.38E−06	5.18E−06	8		0.031	0.031	1.000
cg23130651	− 0.003; − 0.019	− 0.203	2.40E−06	3.14E−06	10	COMMD3	0.883	0.871	9.54E−11
cg03551401	− 0.019; − 0.055	− 0.208	3.46E−06	0.286	8	ADCY8	0.457	0.512	8.35E−53
cg00083685	0.007; 0.033	0.206	3.62E−06	0.114	21	TFF2	0.924	0.927	0.497
cg16198723	− 0.009; − 0.043	− 0.202	3.96E−06	0.001	3	CCDC80	0.600	0.598	1.000
cg02614024	− 0.026; 0.014	− 0.207	4.18E−06	0.733	15		0.194	0.200	1.000
cg23972915	− 0.007; − 0.047	− 0.201	4.27E−06	4.14E−04	14		0.643	0.648	0.509
cg03351418	0.012; 0.008	0.202	8.55E−06	1.000	6	SHPRH	0.841	0.842	1.000
PA—Males
cg06096446	0.014; 0.012	0.204	1.22E−07	1.000	6	TULP4	0.719	0.697	4.02E−07
cg09303847	0.003; 0.003	0.173	9.85E−06	1.000	6		0.042	0.033	1.92E−20
PA—Females
cg17382841	− 0.009; − 0.01	− 0.166	2.74E−06	1.000	5	EGFLAM	0.807	0.792	0.001
cg09179916	− 0.01; − 0.003	− 0.163	3.96E−06	1.000	5	EGFLAM	0.919	0.911	0.004

*Standardised effect sizes ranging from − 1 to 1 obtained from the fixed effect meta-analysis of 450 K and EPIC datasets
^‡Benjamini‒Hochberg corrected p value of the heterogeneity test statistic (Q) on the meta-analysis between 450 K and EPIC platforms
^†Methylation Mean Beta Value
^§The p value of the Wilcoxon two-sample test was corrected using the Bonferroni method

Back to article page

ISSN: 1868-7083

Contact us

Submission enquiries: avalyn.villar@springernature.com
General enquiries: info@biomedcentral.com