High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis

Table 3 DMRs identified after cell type correction

DMR name	Chromosome	Start	End	nprobes	FWER average	FWER maximum	FWER area	Permuted p value	Type
DMR1	Chr5	140582954	140584018	31	<0.01	<0.05	*<0.005*	0.06	TS1
DMR2	Chr11	74630937	74631216	7	<0.05	<0.01	<0.1	0. 03	TS1
DMR3	ChrX	51087402	51089195	32	<0.1	<0.1	<0.01	0. 03	TS1
DMR4	Chr14	54101669	54102157	6	<0.1	<0.1		0.03	TS1
DMR5	Chr2	85215637	85215811	6	<0.1			0.06	TS1
DMR6	Chr14	96038274	96038760	11		<0.01		0.06	TS1
DMR7	Chr9	4731364	4731640	6		<0.05		0.03	TS1
DMR8	Chr1	198645284	198645642	7		<0.1		0.03	TS1
DMR9	Chr1	116184060	116185215	33			<0.05	0.06	TS1
DMR10	Chr15	75897924	75898101	6		<0.05		0.01	TS1
DMR11	Chr2	171280327	171280711	10	<0.1			0.03	TS1
DMR12	Chr16	66835947	66836364	12		<0.05		0.09	TS1
DMR13	Chr13	113192663	113193262	8		<0.1		0.06	TS1
DMR14	Chr22	19603181	19604444	33			<0.1	0.06	TS1
DMR15	Chr17	41620864	41621503	16			<0.1	0.06	TS1
DMR16	Chr8	61353541	61354034	15			<0.1	0.06	TS1
DMR17	ChrX	113720992	113721797	22			<0.1	0.06	TS1
DMR18	Chr10	99200020	99200806	23	<0.05	<0.05	*<0.005*	<0.01	TS2

DMRs (differentially methylated probes) identified after cell type correction in TS1 and TS2; the double criteria for selection is first a FWER <0.20 in at least one of the three statistics (italics) and secondly a permuted p value <0.1. “Start” and “End” denote the start and end location of the DMR in the chromosome. “nprobes” denotes the number of probes in the DMR. “FWER average”, “FWER maximum”, and “FWER area” denote the FWER associated with each one of the statistics used (see “Methods”). “Permuted p value” denotes the p value computed for each DMR locally, comparing each DMR statistic to random permutations of the samples. “Type” denotes if the DMR is associated with TS1 (ACPA/healthy discordant) or TS2 (ACPA-positive RA/healthy discordant). Bold highlights DMRs whose FWER was <0.005. Chromosomal locations are based on the hg18 build

ISSN: 1756-994X