Comparison of methylation capture sequencing and Infinium MethylationEPIC array in peripheral blood mononuclear cells

Shu, Chang; Zhang, Xinyu; Aouizerat, Bradley E.; Xu, Ke

doi:10.1186/s13072-020-00372-6

Epigenetics & Chromatin

Table 4 Discordant CpG sites between MC-seq and EPIC (difference>0.5)

From: Comparison of methylation capture sequencing and Infinium MethylationEPIC array in peripheral blood mononuclear cells

Probe	Chr	Position	Gene	MC-seq median	EPIC median	Median Difference between MC-seq and EPIC	Refgene group	Relation to CpG island
cg09156519	9	103361572		0.009	0.960	0.95		S_Shore
cg18176117	9	96097296	C9orf129	0.000	0.932	0.93	Body	N_Shore
cg14268958	10	133453066		0.000	0.899	0.89		S_Shelf
cg10576280	10	124133822	PLEKHA1	0.072	0.948	0.88	TSS1500	N_Shore
cg01005486	3	13246006		0.047	0.886	0.84		Island
cg23433318	19	667542		0.007	0.866	0.84		Island
cg10766172	7	27498479		0.989	0.147	0.82
cg11812439	4	68928706	LOC550113;SYT14P1;TMPRSS11F	0.973	0.155	0.82	Body; Body; Body
cg23950473	5	154393265	KIF4B; KIF4B	0.992	0.174	0.82	1stExon; 5’UTR
cg00259849	8	4183880	CSMD1	0.000	0.821	0.82	Body
cg23981150	1	161111090		1.000	0.217	0.78		Island
cg09698465	12	133000178		0.906	0.080	0.78		Island
cg20450977	11	10529463	MTRNR2L8; MTRNR2L8	0.964	0.189	0.77	3’UTR; 1stExon
cg01053463	1	26186087	C1orf135	0.021	0.757	0.76	TSS1500	Island
cg12499827	2	202004893	CFLAR; CFLAR; CFLAR; CFLAR; CFLAR; CFLAR; CFLAR; CFLAR; CFLAR	0.971	0.215	0.76	TSS200; Body; Body; Body; Body; Body; Body; Body; Body
cg03133777	2	170361364	BBS5	1.000	0.244	0.75	3’UTR
cg19040702	17	22023833		0.969	0.230	0.75
cg21675871	11	69813397		0.217	0.960	0.74		Island
cg04240493	3	148414664	AGTR1; AGTR1; AGTR1; AGTR1	0.979	0.258	0.72	TSS1500; TSS1500; TSS1500; TSS1500	N_Shore
cg16889427	10	127584375	FANK1	0.036	0.759	0.71	TSS1500	Island
cg25916505	18	32820654	ZNF397; ZNF397	0.000	0.711	0.71	TSS1500; TSS1500	N_Shore
cg13525026	17	18061071	MYO15A	1.000	0.290	0.71	Body
cg07825433	4	1215099	CTBP1; CTBP1	0.000	0.716	0.71	Body; Body	N_Shelf
cg03846641	2	109746751	LOC100287216; SH3RF3	0.239	0.952	0.71	TSS200; Body	Island
cg19188207	2	10340837	C2orf48	1.000	0.290	0.71	Body
cg11495544	17	73402155	GRB2; GRB2	0.753	0.049	0.70	TSS1500; TSS1500	S_Shore
cg06931905	8	42036940	PLAT; PLAT	0.896	0.197	0.70	Body; Body
cg03348902	1	569603		0.869	0.168	0.70
cg27120934	6	129480619	LAMA2; LAMA2	0.979	0.297	0.69	Body; Body
cg07576219	1	55012408	ACOT11; ACOT11	0.927	0.250	0.69	TSS1500; TSS1500	S_Shelf
cg08400246	5	156570642	MED7; MED7	0.153	0.870	0.68	TSS1500; TSS1500	S_Shore
cg27626141	8	103876469	AZIN1; AZIN1	0.000	0.682	0.68	TSS200; TSS200	Island
cg26688472	2	203638928	ICA1L	0.984	0.303	0.68	3’UTR	Island
cg26101183	10	65930786		0.957	0.279	0.68		Island
cg27090007	13	28519388	ATP5EP2	0.985	0.321	0.67	Body
cg11896012	19	53696753	ZNF665	0.048	0.700	0.67	TSS200	S_Shore
cg02606018	12	10658281		0.979	0.323	0.66
cg00438164	4	100870480	H2AFZ; LOC256880	0.004	0.650	0.65	Body; TSS1500	Island
cg21164300	9	136098495		0.000	0.644	0.64		N_Shelf
cg15891076	10	65930618		0.971	0.328	0.64		Island
cg05948389	5	1641924		0.014	0.660	0.64		N_Shelf
cg10507965	10	102107251	SCD; SCD	0.011	0.642	0.64	5’UTR; 1stExon	Island
cg21662326	11	14521493	COPB1; COPB1; COPB1	0.643	0.012	0.63	TSS200; TSS200; TSS200
cg09646578	8	5019363		0.310	0.934	0.63
cg24717964	20	61477008	DPH3B; DPH3B; TCFL5	0.986	0.356	0.63	1stExon; 5’UTR; Body
cg07437919	8	142234483	SLC45A4	0.957	0.313	0.63	Body	N_Shore
cg01105403	2	240723304		0.050	0.890	0.63
cg20482143	7	64340804		0.982	0.346	0.63
cg11187452	22	49698612		0.017	0.653	0.63		Island
cg24504954	3	61237217	FHIT; FHIT	0.017	0.649	0.62	TSS200; TSS200	Island
cg27434351	11	14521491	COPB1; COPB1; COPB1	0.639	0.016	0.62	TSS200; TSS200; TSS200
cg15864074	2	120974042		0.976	0.354	0.62
cg00913521	12	89893799	WDR51B	0.977	0.339	0.62	Body
cg27534567	1	568536		0.834	0.262	0.62
cg24515136	17	49024834		0.949	0.328	0.62		S_Shelf
cg01417615	1	52456419	RAB3B	0.629	0.015	0.61	TSS200	Island
cg00236302	12	69004867	RAP1B; RAP1B	0.000	0.612	0.61	5’UTR; 5’UTR	Island
cg10747603	22	29197018	XBP1; XBP1	0.022	0.627	0.61	TSS1500; TSS1500	S_Shore
cg03594447	1	20359744		1.000	0.358	0.61
cg23045277	4	190587808		0.299	0.910	0.61
cg02218809	16	29973300	TMEM219; TMEM219	0.020	0.612	0.61	TSS200; TSS200	Island
cg05646491	10	135379754	SYCE1; SYCE1; SYCE1	0.988	0.382	0.60	TSS1500; 5’UTR; TSS1500	Island
cg07596174	20	55926107	RAE1; RAE1	0.014	0.613	0.60	TSS1500; TSS200	N_Shore
cg03543448	16	4384967	GLIS2	0.927	0.315	0.60	Body
cg25793197	5	31923469	PDZD2	0.976	0.379	0.60	Body
cg21392229	2	161223778	RBMS1; RBMS1	1.000	0.384	0.60	Body; Body
cg05607320	12	53342553	KRT18; KRT18	0.064	0.651	0.60	TSS200; TSS1500	N_Shore
cg13896861	9	94878241	SPTLC1; SPTLC1	0.117	0.711	0.60	TSS1500; TSS1500	S_Shore
cg03064900	4	190566141		0.323	0.921	0.60		N_Shore
cg16199859	3	75263685		0.861	0.276	0.60
cg15006843	1	205720633	NUCKS1	0.880	0.260	0.60	TSS1500	S_Shore
cg02498218	4	26361371	RBPJ; RBPJ; RBPJ; RBPJ	0.979	0.388	0.59	Body; Body; 5’UTR; Body	Island
cg07116712	15	96887959		0.091	0.681	0.59		Island
cg11643306	20	34204831	SPAG4	0.038	0.630	0.59	Body	S_Shore
cg08568561	7	42834498		0.981	0.392	0.59
cg06669598	6	127622363	ECHDC1; ECHDC1; ECHDC1; ECHDC1; ECHDC1	0.984	0.351	0.59	3’UTR; 3’UTR; Body; Body; Body
cg22805431	3	113955600	ZNF80	0.983	0.409	0.59	1stExon
cg24636332	17	4437925	SPNS2	0.301	0.939	0.59	Body	N_Shore
cg05924191	15	35279830	ZNF770	0.008	0.605	0.59	5’UTR	N_Shore
cg14402194	14	23398944	PRMT5; PRMT5; PRMT5; PRMT5; PRMT5; PRMT5; LOC101926933	0.028	0.592	0.58	TSS200; TSS200; TSS200; TSS200; TSS200; TSS200; Body	S_Shore
cg01737532	4	190862170	FRG1	0.000	0.584	0.58	1stExon	Island
cg25744017	15	52819324	MYO5A; MYO5A	0.957	0.379	0.58	Body;Body	N_Shore
cg03432151	15	89745000	ABHD2; ABHD2	0.948	0.360	0.58	3’UTR; 3’UTR
cg27196695	10	134571377	INPP5A	1.000	0.420	0.58	Body
cg27571351	10	17619364		0.986	0.407	0.58
cg02775804	2	120974080		0.977	0.401	0.58
cg16461530	10	134798264		0.664	0.106	0.58
cg12654770	10	52487693		0.962	0.385	0.58
cg16112880	1	201123745	TMEM9	0.003	0.579	0.58	TSS200	Island
cg20641423	8	125315065		0.911	0.338	0.57		S_Shore
cg23248615	10	2005709		0.905	0.313	0.57
cg25550279	7	53254983		0.965	0.381	0.57		Island
cg01070250	1	569687		0.843	0.271	0.57
cg06977575	4	139481990		0.953	0.376	0.57		Island
cg14511644	9	15055021		0.977	0.399	0.57
cg08947542	8	35383200	UNC5D	0.879	0.309	0.57	Body
cg10258063	2	217363243	RPL37A	0.043	0.613	0.57	TSS1500	N_Shore
cg24209723	18	12913133		0.973	0.399	0.57		S_Shore
cg02265379	5	87898506	LOC645323	0.971	0.384	0.57	Body	Island
cg18925601	7	158752715		0.006	0.574	0.57		Island
cg01406075	11	58731104		0.885	0.309	0.57		N_Shore
cg13545297	12	54404315	HOXC8	0.229	0.791	0.57	Body	S_Shore
cg09036531	10	96991505		0.968	0.402	0.57
cg25649283	9	140714075	EHMT1	0.382	0.950	0.57	Body	Island
cg06204030	17	7792051	CHD3; CHD3; CHD3	0.761	0.141	0.57	TSS200; TSS200; Body	S_Shelf
cg18627328	19	621561	POLRMT	0.980	0.411	0.56	Body	Island
cg13085681	8	48920761	UBE2V2	0.009	0.576	0.56	TSS1500	N_Shore
cg00999469	6	25107287	CMAHP	0.043	0.931	0.56	Body
cg20960039	9	130213605	LRSAM1; RPL12; LRSAM1; LRSAM1; LRSAM1; RPL12	0.020	0.582	0.56	TSS1500; 1stExon; TSS200; TSS200; TSS200; 5’UTR	Island
cg04400841	2	208988863	CRYGD	0.215	0.764	0.56	Body	Island
cg12476298	19	58426697	ZNF417	0.977	0.407	0.56	Body	N_Shore
cg23997402	19	14275669	LPHN1; LPHN1	0.972	0.442	0.56	Body; Body	S_Shore
cg16935370	5	154393281	KIF4B; KIF4B	0.981	0.414	0.56	1stExon; 5′UTR
cg04222159	1	204981786	NFASC; NFASC; NFASC; NFASC	0.630	0.073	0.56	Body; Body; Body; Body
cg06396237	8	120779442	TAF2	0.985	0.430	0.56	Body
cg06599543	6	165749446	PDE10A;PDE10A	0.857	0.332	0.56	Body;Body	S_Shore
cg11566832	10	88659593	BMPR1A	0.145	0.693	0.55	Body
cg20334010	15	41047916	RMDN3; RMDN3	0.020	0.570	0.55	TSS1500; TSS1500	S_Shore
cg18245781	5	3659697		0.283	0.852	0.55
cg03761810	2	10264850	RRM2; RRM2	0.018	0.567	0.55	Body; Body	S_Shore
cg02122372	3	149657597	RNF13; RNF13	1.000	0.439	0.55	Body; Body
cg06753227	18	9475508	RALBP1	0.000	0.553	0.55	TSS200	Island
cg14131834	13	45914250	LOC100190939; TPT1	0.040	0.594	0.55	TSS1500; Body	N_Shore
cg25583180	5	177614382	GMCL1L	1.000	0.451	0.55	Body	Island
cg09112623	6	33756905	LEMD2; LEMD2	0.568	0.019	0.55	5’UTR; 1stExon	Island
cg11759477	4	190861959	FRG1	0.000	0.548	0.55	TSS200	Island
cg12796755	14	51132292	SAV1	0.932	0.383	0.55	Body	N_Shelf
cg19693446	14	102144192		0.958	0.407	0.55
cg25187648	3	49395165	GPX1; GPX1; GPX1	0.018	0.568	0.55	Body; 3’UTR; 1stExon	Island
cg20391833	6	167116208	RPS6KA2	0.964	0.431	0.55	Body
cg09705232	6	97611802	MIR548H3; C6orf167	0.974	0.428	0.55	Body; Body
cg04643437	12	14518655	ATF7IP; ATF7IP	0.000	0.561	0.55	1stExon; 5’UTR	Island
cg17558062	13	45965415	LOC100190939	1.000	0.456	0.54	Body	Island
cg26825848	4	190566175		0.350	0.899	0.54		N_Shore
cg13943141	9	93205862		0.846	0.296	0.54
cg26951705	19	56612697	ZNF787	0.000	0.542	0.54	Body	Island
cg24654094	1	160340832	NHLH1	0.964	0.433	0.54	Body	Island
cg02996355	14	81879375		0.909	0.364	0.54
cg11914812	12	56904792		1.000	0.459	0.54
cg24895977	19	35861796		0.990	0.450	0.54
cg11637682	6	147124984	LOC729176; C6orf103	0.867	0.300	0.54	TSS200; Body
cg07089633	14	73396378	DCAF4; DCAF4; DCAF4; DCAF4; DCAF4	1.000	0.450	0.54	5’UTR; 5’UTR; 5’UTR; 5’UTR; 5’UTR	S_Shelf
cg20360416	4	7246127	SORCS2	0.018	0.659	0.54	Body
cg25627920	17	39992620	NT5C3B; NT5C3B; NT5C3B; KLHL10	0.016	0.552	0.54	TSS200; TSS200; TSS200; TSS1500	Island
cg24000259	5	55488291	ANKRD55	0.961	0.411	0.54	Body
cg09138437	11	64527189	PYGM; PYGM	0.993	0.445	0.54	1stExon; 1stExon
cg02673636	1	109647056		0.976	0.437	0.54		S_Shelf
cg18740872	5	39220260	FYB; FYB	1.000	0.466	0.53	TSS1500; TSS1500
cg14354292	7	63353606		0.960	0.426	0.53
cg17704839	19	9939038	UBL5; UBL5	0.014	0.542	0.53	Body; Body	S_Shore
cg05971373	7	157498604	PTPRN2; PTPRN2; PTPRN2	1.000	0.467	0.53	Body; Body; Body	S_Shelf
cg05291429	17	1494566	SLC43A2	0.402	0.969	0.53	Body	S_Shelf
cg08841342	3	156528470	PA2G4P4	0.976	0.444	0.53	Body
cg04096697	6	37012867		0.983	0.451	0.53		Island
cg26878995	1	168106731	GPR161	0.052	0.570	0.53	TSS1500	S_Shore
cg24031524	20	19804606		0.990	0.468	0.53
cg19311470	4	39460490	RPL9; RPL9; LIAS; LIAS	0.004	0.529	0.53	TSS1500; 5’UTR; TSS200; TSS200	Island
cg02181482	5	178942685		0.956	0.449	0.53
cg05346902	19	47910374	MEIS3; MEIS3	0.068	0.593	0.53	Body; Body	Island
cg16470772	10	8203304		0.971	0.445	0.53
cg10115022	1	27527942		0.974	0.464	0.53		Island
cg27231717	6	26319377		0.905	0.386	0.53
cg09451549	19	8386408	RPS28; NDUFA7; RPS28	0.000	0.527	0.53	5’UTR; TSS200; 1stExon	Island
cg07628841	2	27851430	GPN1; CCDC121; GPN1; GPN1; CCDC121; CCDC121; GPN1; GPN1	0.010	0.536	0.53	TSS200; 1stExon; TSS200; TSS1500; 5’UTR; 1stExon; TSS200; TSS1500
cg03816081	10	29577743	LYZL1	0.863	0.301	0.52	TSS1500
cg00762003	21	45393541	AGPAT3; AGPAT3	0.383	0.892	0.52	Body; Body	Island
cg19466922	7	130138026	MEST; MEST; MEST; MEST; MEST; MEST	1.000	0.476	0.52	Body; Body; Body; Body; Body; Body
cg07712165	17	80899280	TBCD	0.440	0.959	0.52	Body	Island
cg01199952	13	25591486		0.984	0.456	0.52		N_Shore
cg11374834	3	75263691		0.950	0.428	0.52
cg02974491	1	1162280	SDF4; SDF4	0.403	0.964	0.52	Body; Body	Island
cg10555853	1	33516627		0.929	0.407	0.52		Island
cg21216606	2	207275704		0.985	0.464	0.52
cg17711541	6	26124704	HIST1H2AC; HIST1H2BC	0.007	0.529	0.52	1stExon; TSS1500	Island
cg06412823	7	22541074	STEAP1B; STEAP1B	0.196	0.739	0.52	TSS1500; TSS1500	S_Shore
cg03054343	11	50238214		1.000	0.463	0.52		Island
cg05766605	1	19384827		0.423	0.938	0.52
cg07684215	10	132976057	TCERG1L	0.181	0.923	0.52	Body
cg27193858	6	41169120	TREML2	0.181	0.691	0.52	TSS200
cg00964321	16	15083956	PDXDC1	0.906	0.386	0.52	Body	Island
cg25394572	11	56457777	OR8U8	0.949	0.429	0.52	Body
cg10667969	3	149181941		0.967	0.458	0.52
cg18394854	5	8457818		0.212	0.732	0.52		Island
cg05741225	10	133917303	JAKMIP3	0.906	0.370	0.52	TSS1500
cg06026769	12	20704492	PDE3A	0.993	0.473	0.52	Body	N_Shore
cg09032630	6	27831956	HIST1H2AL	0.802	0.311	0.52	TSS1500	N_Shore
cg16626480	22	25575426	KIAA1671	0.950	0.422	0.52	Body	Island
cg24534731	17	36888147	CISD3	0.969	0.457	0.52	Body	S_Shore
cg16202259	14	104625420	KIF26A	0.058	0.962	0.52	Body	Island
cg25325592	8	1439535		0.408	0.923	0.52		N_Shore
cg00391025	3	100427239	TFG; TFG	1.000	0.477	0.52	TSS1500; TSS1500	N_Shore
cg25149037	17	39736213		0.820	0.454	0.52
cg19120749	11	1431650	BRSK2; BRSK2; BRSK2; BRSK2; BRSK2; BRSK2	0.468	0.983	0.52	TSS1500; TSS200; Body; Body; Body; Body	Island
cg24270624	10	95721318	PIPSL	0.947	0.421	0.52	Body
cg16346588	10	242978	ZMYND11; ZMYND11; ZMYND11	0.970	0.459	0.51	Body; Body; Body
cg02750322	15	83673816	C15orf40; C15orf40; C15orf40; C15orf40; C15orf40	0.966	0.451	0.51	Body; 3’UTR; Body; Body; Body
cg04363536	3	49466872	NICN1	0.000	0.515	0.51	TSS200	S_Shore
cg17883371	1	91359225		1.000	0.480	0.51		Island
cg25018832	1	564471	LOC101928626	0.602	0.088	0.51	TSS200
cg16838729	4	43901032		0.903	0.394	0.51
cg23222247	17	47302219	PHOSPHO1; PHOSPHO1	0.009	0.531	0.51	Body;Body	Island
cg19496566	19	48249018	GLTSCR2	0.009	0.535	0.51	1stExon	Island
cg03165426	7	30726958	CRHR2; CRHR2	0.429	0.942	0.51	Body; 5’UTR
cg19600494	2	106959525		0.968	0.455	0.51		Island
cg10854807	17	79479308	ACTG1	0.004	0.522	0.51	Body	Island
cg20699097	11	111957680	TIMM8B; TIMM8B; SDHD	0.009	0.524	0.51	TSS200; TSS200; 1stExon	Island
cg22819767	10	11866910	C10orf47	0.958	0.440	0.51	5’UTR	S_Shore
cg20254251	8	144557206	ZC3H3	0.993	0.450	0.51	Body
cg00590830	1	32385224	PTP4A2; PTP4A2; PTP4A2; PTP4A2; PTP4A2	0.971	0.437	0.51	1stExon; 1stExon; 5’UTR; 5’UTR; 5’UTR
cg03877767	2	11680057	GREB1; GREB1	0.172	0.683	0.51	5’UTR; TSS200
cg00487526	15	90818384		0.956	0.444	0.51		Island
cg17501384	2	217364031	RPL37A	0.017	0.521	0.51	Body	S_Shore
cg17646418	6	166911767	RPS6KA2; RPS6KA2	0.987	0.468	0.51	Body; Body
cg06757405	5	140789450	PCDHGA4; PCDHGA9; PCDHGA1; PCDHGB1; PCDHGB6; PCDHGB6; PCDHGB3; PCDHGA6; PCDHGA8; PCDHGA5; PCDHGB4; PCDHGA3; PCDHGA2; PCDHGB2; PCDHGA7; PCDHGB5	0.108	0.607	0.51	Body; Body; Body; Body; 1stExon; 1stExon; Body; Body; Body; Body; Body; Body; Body; Body; Body; Body	Island
cg13448596	8	2031599	MYOM2	0.381	0.887	0.51	Body
cg16711165	11	111957658	TIMM8B; TIMM8B; SDHD	0.017	0.522	0.51	TSS200; TSS200; 1stExon	Island
cg16786640	4	3485263	DOK7; DOK7	0.447	0.954	0.51	Body; Body	N_Shore
cg07638938	10	131348599	MGMT	0.986	0.492	0.51	Body
cg05407710	8	143329409	TSNARE1	0.960	0.451	0.51	Body	N_Shelf
cg07869994	3	174095190		0.988	0.482	0.51		Island
cg07455406	14	21077527		0.017	0.523	0.51		N_Shore
cg04576847	17	12623611	MYOCD; MYOCD; MYOCD; MYOCD	0.958	0.447	0.51	Body; 5’UTR; Body; 1stExon
cg15699853	18	57684747		0.976	0.467	0.51
cg11231240	8	82434638		1.000	0.482	0.51		Island
cg06157924	4	942005	TMEM175	0.451	0.957	0.51	Body	S_Shore
cg23679141	4	165118930	MARCH1; ANP32C	0.946	0.445	0.51	5’UTR; TSS200
cg03053358	17	1029917	ABR; ABR	0.446	0.964	0.51	Body; 5’UTR	S_Shore
cg13705894	9	138305338		0.978	0.495	0.51		S_Shore
cg18512780	17	76117734	TMC6; TMC6	0.033	0.529	0.50	Body; Body
cg06307940	16	46660818		0.986	0.487	0.50
cg15541008	5	95297508	ELL2; ELL2	0.000	0.516	0.50	1stExon; 5’UTR	S_Shore
cg19969624	13	95954210	ABCC4; ABCC4; ABCC4; ABCC4	0.011	0.507	0.50	TSS1500; TSS1500; TSS1500; TSS1500	Island
cg01758870	7	23719630	C7orf46; C7orf46; C7orf46	0.028	0.545	0.50	TSS200;TSS200;TSS200	Island
cg08323201	15	101835348	SNRPA1	0.000	0.503	0.50	1stExon	Island
cg21863998	11	19770288	NAV2; NAV2; NAV2	0.439	0.905	0.50	Body; Body; Body
cg11471802	8	47529015		0.348	0.882	0.50		Island
cg22281935	2	162934111		0.982	0.481	0.50		S_Shelf
cg06032540	15	43941563	CATSPER2; CATSPER2; CATSPER2	1.000	0.500	0.50	TSS1500; TSS1500; TSS1500	Island
cg18761878	1	568475		0.893	0.401	0.50

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