Methylomic markers of persistent childhood asthma: a longitudinal study of asthma-discordant monozygotic twins

Therese M. Murphy; Chloe C. Y. Wong; Louise Arseneault; Joe Burrage; Ruby Macdonald; Eilis Hannon; Helen L. Fisher; Antony Ambler; Terrie E. Moffitt; Avshalom Caspi; Jonathan Mill

doi:10.1186/s13148-015-0163-4

Clinical Epigenetics

Table 2 The top-ranked DMPs in age-10 MZ twins persistently discordant for asthma

From: Methylomic markers of persistent childhood asthma: a longitudinal study of asthma-discordant monozygotic twins

	Age 10					Age 5
Probe ID	Co-twin mean	Asthma mean	Mean ∆β	P value	Empirical P value	Mean ∆β	P value	Relation to CpG island	Gene region feature category (UCSC)	Hg19	Illumina gene annotation	Probe type	Gene annotation from GREAT (distance from TSS)
cg23603194	0.289	0.180	−0.109	6.87E-06	0.0009	0.056	0.0519	N_Shore	Intergenic	Chr1:221060753		II	HLX (+8011), DUSP10 (+854762)
cg27385757	0.353	0.286	−0.067	2.16E-05	0.0012	0.029	0.1966	S_Shore	TSS1500; 3′UTR	Chr6:30656024	KIAA1949; NRM	II	PPP1R18 (−932)
cg06483698	0.805	0.848	0.043	2.64E-05	0.0007	−0.006	0.6847	N_Shore	Body	Chr7:6310290	CYTH3	II	CYTH3 (+1951), USP42 (+165741)
cg05895618	0.559	0.655	0.096	2.69E-05	0.0007	−0.026	0.5367		5′UTR	Chr11:19222395	CSRP3	II	CSRP3 (+1193), ZDHHC13 (+83704)
cg14868530	0.081	0.098	0.017	3.36E-05	0.0005	−0.008	0.0351	Island	5′UTR; 1stExon	Chr15:73976679	CD276	I	CD276 (+58)
cg21304454	0.530	0.392	−0.138	3.59E-05	0.0009	0.070	0.1223	N_Shelf	Body	Chr1:17302859	MFAP2	II	MFAP2 (+4313), CROCC (+54415)
cg11998205	0.853	0.806	−0.047	4.28E-05	0.0017	−0.033	0.0361	S_Shelf	Body	Chr19:48840527	TMEM143	I	EMP3 (+11899), TMEM143 (+26658)
cg18513344	0.210	0.137	−0.072	4.39E-05	0.0007	−0.022	0.3459		Body	Chr3:195531298	MUC4	II	MUC4 (+7545), MUC20 (+83546)
cg08657206	0.256	0.221	−0.035	5.55E-05	0.0009	−0.005	0.7971	N_Shore	Intergenic	Chr1:180197901		I	LHX4 (−1531)
cg19865472	0.897	0.844	−0.052	5.90E-05	0.0004	−0.065	0.1373	Island	3′UTR	Chr19:617133	HCN2	I	POLRMT (+16434), HCN2 (+27241)
cg26280666	0.0976	0.0717	−0.0259	6.13E-05	0.0009	−0.0115	0.4006	N_Shore	Body	Chr8:72755568	MSC	II	EYA1 (−486590), MSC (+1162)
cg13512987	0.5252	0.6452	0.1200	6.77E-05	0.0005	−0.0438	0.1137		5′UTR; 1stExon	Chr12:6898785	CD4	II	CD4 (+148)
cg24664347	0.7364	0.8161	0.0797	7.51E-05	0.0006	−0.0624	0.0007	S_Shore	TSS1500	Chr8:86841010	REXO1L2P	II	REXO1L1 (−51705), PSKH2 (+240840)
cg25346117	0.6694	0.7450	0.0756	8.06E-05	0.0004	0.0030	0.8688		Body	Chr1:116923256	ATP1A1	II	ATP1A1 (+7462), CD58 (+190458)
cg09587549	0.2320	0.2647	0.0327	9.75E-05	0.0005	−0.0006	0.9742	Island	5′UTR; 1stExon	Chr16:31214126	PYCARD	I	PYCARD (−30)
cg03225548	0.7651	0.6807	−0.0844	9.90E-05	0.0004	−0.0014	0.9638	N_Shelf	Body; 5′UTR	Chr18:71811234	FBXO15	II	TIMM21 (−4511), FBXO15 (+3865)
cg17130754	0.7563	0.6967	−0.0597	9.99E-05	0.0004	0.0478	0.0739		Intergenic	Chr10:3536341		II	PITRM1 (−321309), KLF6 (+291131)

Ranked by P value. Empirical P value = (number of permutations which are at least as significant as the true result (P < 0.0001) divided by the number of permutations performed (n = 8192))
DMPs differentially methylated positions, MZ monozygotic, GREAT Genomic Regions Enrichment of Annotations Tool, TSS transcription start site, UCSC University of California Santa Cruz genome browser

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